       1 #!/usr/bin/perl -w
       2 #
       3 # $RCSfile: TextFilesToSDFiles.pl,v $
       4 # $Date: 2015/02/28 20:46:21 $
       5 # $Revision: 1.25 $
       6 #
       7 # Author: Manish Sud <msud@san.rr.com>
       8 #
       9 # Copyright (C) 2015 Manish Sud. All rights reserved.
      10 #
      11 # This file is part of MayaChemTools.
      12 #
      13 # MayaChemTools is free software; you can redistribute it and/or modify it under
      14 # the terms of the GNU Lesser General Public License as published by the Free
      15 # Software Foundation; either version 3 of the License, or (at your option) any
      16 # later version.
      17 #
      18 # MayaChemTools is distributed in the hope that it will be useful, but without
      19 # any warranty; without even the implied warranty of merchantability of fitness
      20 # for a particular purpose.  See the GNU Lesser General Public License for more
      21 # details.
      22 #
      23 # You should have received a copy of the GNU Lesser General Public License
      24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
      25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
      26 # Boston, MA, 02111-1307, USA.
      27 #
      28
      29 use strict;
      30 use FindBin; use lib "$FindBin::Bin/../lib";
      31 use Getopt::Long;
      32 use File::Basename;
      33 use Text::ParseWords;
      34 use Benchmark;
      35 use FileUtil;
      36 use TextUtil;
      37 use SDFileUtil;
      38
      39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      40
      41 # Autoflush STDOUT
      42 $| = 1;
      43
      44 # Starting message...
      45 $ScriptName = basename $0;
      46 print "\n$ScriptName:Starting...\n\n";
      47 $StartTime = new Benchmark;
      48
      49 # Get the options and setup script...
      50 SetupScriptUsage();
      51 if ($Options{help} || @ARGV < 1) {
      52   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      53 }
      54
      55 my(@TextFilesList);
      56 @TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
      57
      58 print "Processing options...\n";
      59 my(%OptionsInfo);
      60 ProcessOptions();
      61
      62 print "Checking input text file(s)...\n";
      63 my(%TextFilesInfo);
      64 RetrieveTextFilesInfo();
      65
      66 # Generate output files...
      67 my($FileIndex);
      68 if (@TextFilesList > 1) {
      69   print "\nProcessing text files...\n";
      70 }
      71 for $FileIndex (0 .. $#TextFilesList) {
      72   if ($TextFilesInfo{FileOkay}[$FileIndex]) {
      73     print "\nProcessing file $TextFilesList[$FileIndex]...\n";
      74     ConvertTextFile($FileIndex);
      75   }
      76 }
      77 print "\n$ScriptName:Done...\n\n";
      78
      79 $EndTime = new Benchmark;
      80 $TotalTime = timediff ($EndTime, $StartTime);
      81 print "Total time: ", timestr($TotalTime), "\n";
      82
      83 ###############################################################################
      84
      85 # Convert text file to SD file...
      86 sub ConvertTextFile {
      87   my($Index) = @_;
      88   my($TextFile, $SDFile, $Line, $InDelim, $Label, $Value, $ColIndex, $ColCount, @ColLabels, @LineWords);
      89
      90   $TextFile = $TextFilesList[$Index];
      91   $InDelim = $TextFilesInfo{InDelim}[$Index];
      92   $SDFile = $TextFilesInfo{OutSDFile}[$Index];
      93   @ColLabels = @{$TextFilesInfo{ColLabels}[$Index]};
      94   $ColCount = @ColLabels;
      95
      96   print "Generating SD file $SDFile...\n";
      97   open SDFILE, ">$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
      98   open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n";
      99   if ($OptionsInfo{ColLabelsPresent}) {
     100     # Skip over column labels from old file...
     101     $Line = GetTextLine(\*TEXTFILE);
     102   }
     103   my($Date) = GenerateMiscLineDateStamp();
     104   while ($Line = GetTextLine(\*TEXTFILE)) {
     105     @LineWords = quotewords($InDelim, 0, $Line);
     106
     107     # Write out empty CTAB block...
     108     print SDFILE GenerateEmptyCtabBlockLines($Date), "\n";
     109
     110     # Write out data fields and values...
     111     for $ColIndex (0 .. $#LineWords) {
     112       if ($ColIndex < $ColCount) {
     113         $Label = $ColLabels[$ColIndex];
     114         $Value = $LineWords[$ColIndex];
     115         print SDFILE "> <$Label>\n$Value\n\n";
     116       }
     117     }
     118     print SDFILE "\$\$\$\$\n";
     119   }
     120   close SDFILE;
     121   close TEXTFILE;
     122 }
     123
     124 # Retrieve information about input text files...
     125 sub RetrieveTextFilesInfo {
     126   my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, @LineWords, @ColLabels, $OutFileRoot,  $OutFile, $ColNum, $ColLabel);
     127
     128   %TextFilesInfo = ();
     129
     130   @{$TextFilesInfo{FileOkay}} = ();
     131   @{$TextFilesInfo{ColCount}} = ();
     132   @{$TextFilesInfo{ColLabels}} = ();
     133   @{$TextFilesInfo{InDelim}} = ();
     134   @{$TextFilesInfo{OutSDFile}} = ();
     135
     136
     137   FILELIST: for $Index (0 .. $#TextFilesList) {
     138     $TextFile = $TextFilesList[$Index];
     139
     140     $TextFilesInfo{FileOkay}[$Index] = 0;
     141     $TextFilesInfo{ColCount}[$Index] = 0;
     142     $TextFilesInfo{InDelim}[$Index] = "";
     143     $TextFilesInfo{OutSDFile}[$Index] = "";
     144
     145     @{$TextFilesInfo{ColLabels}[$Index]} = ();
     146
     147     if (!(-e $TextFile)) {
     148       warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
     149       next FILELIST;
     150     }
     151     if (!CheckFileType($TextFile, "csv tsv")) {
     152       warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
     153       next FILELIST;
     154     }
     155     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
     156     if ($FileExt =~ /^tsv$/i) {
     157       $InDelim = "\t";
     158     }
     159     else {
     160       $InDelim = "\,";
     161       if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
     162         warn "Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n";
     163         next FILELIST;
     164       }
     165       if ($Options{indelim} =~ /^semicolon$/i) {
     166         $InDelim = "\;";
     167       }
     168     }
     169     if (!open TEXTFILE, "$TextFile") {
     170       warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
     171       next FILELIST;
     172     }
     173     $Line = GetTextLine(\*TEXTFILE);
     174     @LineWords = quotewords($InDelim, 0, $Line);
     175     @ColLabels = ();
     176     if ($OptionsInfo{ColLabelsPresent}) {
     177       push @ColLabels, @LineWords;
     178     }
     179     else {
     180       for $ColNum (1 .. @LineWords) {
     181         $ColLabel = "Column${ColNum}Data";
     182         push @ColLabels, $ColLabel;
     183       }
     184     }
     185     close TEXTFILE;
     186
     187     $FileDir = ""; $FileName = ""; $FileExt = "";
     188     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
     189     if ($Options{root} && (@TextFilesList == 1)) {
     190       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
     191       if ($RootFileName && $RootFileExt) {
     192         $FileName = $RootFileName;
     193       }
     194       else {
     195         $FileName = $Options{root};
     196       }
     197       $OutFileRoot = $FileName;
     198     }
     199     else {
     200       $OutFileRoot = "${FileName}WithNoStrData";
     201     }
     202
     203     $OutFile = "${OutFileRoot}.sdf";
     204     if (!$Options{overwrite}) {
     205       if (-e $OutFile) {
     206         warn "Warning: Ignoring file $TextFile: The file $OutFile already exists\n";
     207         next FILELIST;
     208       }
     209     }
     210     $TextFilesInfo{FileOkay}[$Index] = 1;
     211     $TextFilesInfo{InDelim}[$Index] = $InDelim;
     212     $TextFilesInfo{OutSDFile}[$Index] = "$OutFile";
     213
     214     $TextFilesInfo{ColCount}[$Index] = @ColLabels;
     215     push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
     216   }
     217 }
     218
     219 # Process option values...
     220 sub ProcessOptions {
     221   %OptionsInfo = ();
     222
     223   $OptionsInfo{Label} = $Options{label};
     224   $OptionsInfo{ColLabelsPresent} = ($Options{label} =~ /^yes$/i) ? 1 : 0;
     225
     226   $OptionsInfo{InDelim} = $Options{indelim};
     227   $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
     228
     229   $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
     230
     231 }
     232
     233 # Setup script usage  and retrieve command line arguments specified using various options...
     234 sub SetupScriptUsage {
     235
     236   # Retrieve all the options...
     237   %Options = ();
     238   $Options{label} = "yes";
     239   $Options{indelim} = "comma";
     240   if (!GetOptions(\%Options, "help|h", "indelim=s", "label|l=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
     241     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     242   }
     243   if ($Options{workingdir}) {
     244     if (! -d $Options{workingdir}) {
     245       die "Error: The value specified, $Options{workingdir},  for option \"-w --workingdir\" is not a directory name.\n";
     246     }
     247     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     248   }
     249   if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
     250     die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n";
     251   }
     252   if ($Options{label} !~ /^(yes|no)$/i) {
     253     die "Error: The value specified, $Options{label}, for option \"-l --label\" is not valid. Allowed values: yes or no\n";
     254   }
     255 }
     256