       1 #!/usr/bin/perl -w
       2 #
       3 # $RCSfile: ModifySDFilesDataFields.pl,v $
       4 # $Date: 2015/02/28 20:46:20 $
       5 # $Revision: 1.27 $
       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 "$FindBin::Bin/../lib";
      31 use Getopt::Long;
      32 use File::Basename;
      33 use Text::ParseWords;
      34 use Benchmark;
      35 use FileUtil;
      36 use SDFileUtil;
      37 use TextUtil;
      38
      39 my($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(@SDFilesList);
      56 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      57
      58 # Process options...
      59 print "Processing options...\n";
      60 my(%OptionsInfo);
      61 ProcessOptions();
      62
      63 print "Checking input SD file(s)...\n";
      64 my(%SDFilesInfo);
      65 RetrieveSDFilesInfo();
      66
      67 # Generate output files...
      68 my($FileIndex);
      69 if (@SDFilesList > 1) {
      70   print "\nProcessing SD files...\n";
      71 }
      72 for $FileIndex (0 .. $#SDFilesList) {
      73   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
      74     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
      75     ModifySDFile($FileIndex);
      76   }
      77 }
      78 print "\n$ScriptName:Done...\n\n";
      79
      80 $EndTime = new Benchmark;
      81 $TotalTime = timediff ($EndTime, $StartTime);
      82 print "Total time: ", timestr($TotalTime), "\n";
      83
      84 ###############################################################################
      85
      86 # Modify SD file data fields....
      87 sub ModifySDFile {
      88   my($Index) = @_;
      89   my($SDFile, $NewSDFile);
      90
      91   $SDFile = $SDFilesList[$Index];
      92   $NewSDFile = $SDFilesInfo{OutFile}[$Index];
      93
      94   print "Generating new SD file $NewSDFile...\n";
      95   open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
      96   open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
      97
      98   my($CmpdCount, $CmpdString, $CmpdData, $MolName, $OldSDField, $NewSDField, $CommonSDField, $Label, $Value, $FieldValues, $MolNameDataField, $URLCmpdIdFieldName, @CmpdLines, %DataFieldAndValues, @DataFieldLabels);
      99   $CmpdCount = 0;
     100
     101   COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
     102       $CmpdCount++;
     103       @CmpdLines = split "\n", $CmpdString;
     104       if ($OptionsInfo{UseDataFieldForMolName} || $OptionsInfo{ModifyDataFields}) {
     105         %DataFieldAndValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     106       }
     107       if ($OptionsInfo{ModifyMolName}) {
     108         if ($OptionsInfo{AlwaysReplaceMolName} || !IsNotEmpty($CmpdLines[0])) {
     109           $MolNameDataField = $OptionsInfo{MolNameDataField};
     110           if ($OptionsInfo{UseDataFieldForMolName} && exists($DataFieldAndValues{$MolNameDataField})) {
     111             $MolName = $DataFieldAndValues{$MolNameDataField};
     112             if (length($MolName) > 80) {
     113               $MolName = substr($MolName, 0, 80);
     114             }
     115           }
     116           else {
     117             $MolName = "$OptionsInfo{MolNamePrefix}${CmpdCount}";
     118           }
     119           $CmpdLines[0] = $MolName;
     120           $CmpdString = join "\n", @CmpdLines;
     121         }
     122       }
     123       if (!$OptionsInfo{ModifyDataFields}) {
     124         # Just write the data and get the next compound...
     125         print NEWSDFILE "$CmpdString\n";
     126         next COMPOUND;
     127       }
     128       # Write out the structure data now and handle the old data fields later...
     129       ($CmpdData) = split /\n>/, $CmpdString;
     130       print NEWSDFILE "$CmpdData\n";
     131
     132       # Modify specified data fields...
     133       for $NewSDField (sort keys %{$OptionsInfo{SpecifiedNewToOldSDFieldMap}}) {
     134         $FieldValues = "";
     135         for $OldSDField (@{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}}) {
     136           if (exists($DataFieldAndValues{$OldSDField}) && length($DataFieldAndValues{$OldSDField})) {
     137             $Value = $DataFieldAndValues{$OldSDField};
     138             $FieldValues .= ($FieldValues) ? "\n$Value" : $Value;
     139           }
     140         }
     141         print NEWSDFILE "> <$NewSDField>\n$FieldValues\n\n";
     142       }
     143       # Add specified common fields...
     144       for $CommonSDField (sort keys %{$OptionsInfo{SpecifiedCommonFieldMap}}) {
     145         $Value = $OptionsInfo{SpecifiedCommonFieldMap}{$CommonSDField};
     146         print NEWSDFILE "> <$CommonSDField>\n$Value\n\n";
     147       }
     148       if ($OptionsInfo{CreateDataFieldURL}) {
     149         $Value = "";
     150         $URLCmpdIdFieldName = $OptionsInfo{URLCmpdIdFieldName};
     151         if (exists($DataFieldAndValues{$URLCmpdIdFieldName}) && length($DataFieldAndValues{$URLCmpdIdFieldName})) {
     152           $Value = $DataFieldAndValues{$URLCmpdIdFieldName};
     153           $Value = "$OptionsInfo{URLCGIScriptName}?$OptionsInfo{URLParamName}=${Value}";
     154         }
     155         print NEWSDFILE "> <$OptionsInfo{URLDataFieldLabel}>\n$Value\n\n";
     156       }
     157
     158       # Handle old data fields and write 'em in the same order as they appear in the input
     159       # files...
     160       if ($OptionsInfo{KeepAllOldDataFields} || $OptionsInfo{KeepUnMappedOldDataFields}) {
     161         my($KeepLabel);
     162         @DataFieldLabels = GetCmpdDataHeaderLabels(\@CmpdLines);
     163         LABEL: for $Label (@DataFieldLabels) {
     164           $KeepLabel = $OptionsInfo{KeepAllOldDataFields} ? 1 : ( exists($OptionsInfo{SpecifiedOldToNewSDFieldMap}{$Label}) ? 0 : 1  );
     165           if (!$KeepLabel) {
     166             next LABEL;
     167           }
     168           $Value = $DataFieldAndValues{$Label};
     169           print NEWSDFILE "> <$Label>\n$Value\n\n";
     170         }
     171       }
     172
     173       print NEWSDFILE "\$\$\$\$\n";
     174   }
     175   close NEWSDFILE;
     176   close SDFILE;
     177 }
     178
     179 # Process option values...
     180 sub ProcessOptions {
     181   %OptionsInfo = ();
     182
     183   $OptionsInfo{Mode} = $Options{mode};
     184
     185   $OptionsInfo{ModifyMolName} = 1; $OptionsInfo{ModifyDataFields} = 0;
     186   if ($Options{mode} =~ /^both$/i) {
     187     $OptionsInfo{ModifyMolName} = 1; $OptionsInfo{ModifyDataFields} = 1;
     188   }
     189   elsif ($Options{mode} =~ /^datafields$/i) {
     190     $OptionsInfo{ModifyMolName} = 0; $OptionsInfo{ModifyDataFields} = 1;
     191   }
     192
     193   $OptionsInfo{KeepOldDataFields} = $Options{keepolddatafields};
     194   $OptionsInfo{KeepAllOldDataFields} = ($Options{keepolddatafields} =~ /^all$/i) ? 1 : 0;
     195   $OptionsInfo{KeepUnMappedOldDataFields} = ($Options{keepolddatafields} =~ /^unmappedonly$/i) ? 1 : 0;
     196
     197   $OptionsInfo{MolNameMode} = $Options{molnamemode};
     198   $OptionsInfo{UseDataFieldForMolName} = ($Options{molnamemode} =~ /^datafield$/i) ? 1 : 0;
     199
     200   $OptionsInfo{MolName} = $Options{molname};
     201   $OptionsInfo{MolNameDataField} = ""; $OptionsInfo{MolNamePrefix} = "Cmpd";
     202   if ($Options{molname}) {
     203     if ($OptionsInfo{UseDataFieldForMolName}) {
     204       $OptionsInfo{MolNameDataField} = $Options{molname};
     205     }
     206     else {
     207       $OptionsInfo{MolNamePrefix} = $Options{molname};
     208     }
     209   }
     210
     211   $OptionsInfo{MolNameReplace} = $Options{molnamereplace};
     212   $OptionsInfo{AlwaysReplaceMolName} = ($Options{molnamereplace} =~ /^always$/i) ? 1 : 0;
     213
     214   if ($Options{datafieldsmap} && $Options{datafieldsmapfile}) {
     215     die "Error: Both \"--datafieldsmap\" and  \"--datafieldsmapfile\" options specified: only one is allowed at a time\n";
     216   }
     217
     218   $OptionsInfo{DataFieldsMap} = $Options{datafieldsmap} ? $Options{datafieldsmap} : '';
     219   $OptionsInfo{DataFieldsMapFile} = $Options{datafieldsmapfile} ? $Options{datafieldsmapfile} : '';
     220
     221   my($SpecifiedDataFieldMap);
     222
     223   %{$OptionsInfo{SpecifiedNewToOldSDFieldMap}} = ();
     224   %{$OptionsInfo{SpecifiedOldToNewSDFieldMap}} = ();
     225
     226   $SpecifiedDataFieldMap = "";
     227   if ($Options{datafieldsmap}) {
     228     $SpecifiedDataFieldMap = $Options{datafieldsmap};
     229   }
     230   elsif ($Options{datafieldsmapfile}) {
     231     my($Line, @LineWords);
     232     open DATAFIELDSFILE, "$Options{datafieldsmapfile}" or die "Couldn't  open $Options{datafieldsmapfile}: $! \n";
     233     while ($Line = GetTextLine(\*DATAFIELDSFILE)) {
     234       @LineWords = quotewords(";", 0, $Line);
     235       $SpecifiedDataFieldMap .= JoinWords(\@LineWords, ";", 0);
     236     }
     237     close DATAFIELDSFILE;
     238   }
     239
     240   if ($SpecifiedDataFieldMap) {
     241     my($DataFieldMap, $DataField, $NewSDField, @OldSDFields, @DataFieldMapSplit, @DataFieldsSplit, $FirstField);
     242     @DataFieldMapSplit = split ";", $SpecifiedDataFieldMap;
     243     for $DataFieldMap (@DataFieldMapSplit) {
     244       @DataFieldsSplit = split ",", $DataFieldMap;
     245       if (@DataFieldsSplit == 1) {
     246         die "Error: Invalid number of comma delimited values, ", scalar(@DataFieldsSplit), ", specified,  @DataFieldsSplit, using \"--datafieldsmap or --datafieldsmapfile\" option: it must contain more than one value.\n";
     247       }
     248       $FirstField = 1;
     249       @OldSDFields = ();
     250       for $DataField (@DataFieldsSplit) {
     251         if (!(defined($DataField) && length($DataField))) {
     252           die "Error: One of the comma delimited values, \"", join(",", @DataFieldsSplit), "\", specified using \"--datafieldsmap or --datafieldsmapfile\" option is empty.\n";
     253         }
     254         if ($FirstField) {
     255           $FirstField = 0;
     256           $NewSDField = $DataField;
     257         }
     258         else {
     259           push @OldSDFields, $DataField;
     260         }
     261       }
     262       # Make sure a datafield is only specified once...
     263       if (exists $OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}) {
     264         die "Error: New data field, $NewSDField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n";
     265       }
     266       @{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}} = ();
     267       push @{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}}, @OldSDFields;
     268       for $DataField (@OldSDFields) {
     269         if (exists $OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataField} ) {
     270           die "Error: SD field, $DataField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n";
     271         }
     272         else {
     273           $OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataField} = $NewSDField;
     274         }
     275       }
     276
     277     }
     278   }
     279
     280   $OptionsInfo{DataFieldsCommon} = $Options{datafieldscommon} ? $Options{datafieldscommon} : '';
     281   %{$OptionsInfo{SpecifiedCommonFieldMap}} = ();
     282
     283   if ($Options{datafieldscommon}) {
     284     my($DataFieldName, $DataFieldValue, $Index, @CommonDataFieldsSplit);
     285     @CommonDataFieldsSplit = split ",", $Options{datafieldscommon};
     286     if (@CommonDataFieldsSplit % 2) {
     287         die "Error: Invalid number of comma delimited values, ", scalar(@CommonDataFieldsSplit), ", specified \"",  join(",", @CommonDataFieldsSplit), "\" using \"--datafieldscommon\" option: it must contain even number of values.\n";
     288     }
     289     for ($Index = 0; $Index < @CommonDataFieldsSplit; $Index += 2) {
     290       $DataFieldName = $CommonDataFieldsSplit[$Index];
     291       $DataFieldValue = $CommonDataFieldsSplit[$Index + 1];
     292       if (exists $OptionsInfo{SpecifiedCommonFieldMap}{$DataFieldName}) {
     293         die "Error: Common data field, $DataFieldName, specified more than once using \"--datafieldscommon\" option.\n";
     294       }
     295       if (exists($OptionsInfo{SpecifiedNewToOldSDFieldMap}{$DataFieldName}) || exists($OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataFieldName})) {
     296         die "Error: Common data field, $DataFieldName, specified using \"--datafieldscommon\" option cannot be specified in \"--datafieldsmap or --datafieldsmapfile\" option.\n";
     297       }
     298       $OptionsInfo{SpecifiedCommonFieldMap}{$DataFieldName} = $DataFieldValue;
     299     }
     300   }
     301
     302   $OptionsInfo{DataFieldURL} = $Options{datafieldurl} ? $Options{datafieldurl} : '';
     303   $OptionsInfo{CreateDataFieldURL} = (exists($Options{datafieldurl}) && length($Options{datafieldurl}) ) ? 1 : 0;
     304
     305   $OptionsInfo{URLDataFieldLabel} = ""; $OptionsInfo{URLCGIScriptName} = "";
     306   $OptionsInfo{URLParamName} = ""; $OptionsInfo{URLCmpdIdFieldName} = "";
     307
     308   if ($OptionsInfo{CreateDataFieldURL}) {
     309     my(@DataFieldURLSplit, $Value);
     310     @DataFieldURLSplit = split ",", $Options{datafieldurl};
     311     if (@DataFieldURLSplit != 4) {
     312       die "Error: Invalid number of values, ", scalar(@DataFieldURLSplit), ", specified using \"--datafieldURL\" option: it must contain 4 values.\n";
     313     }
     314     for $Value (@DataFieldURLSplit) {
     315       if (!IsNotEmpty($Value)) {
     316         die "Error: One of the values, $Options{datafieldurl}, specified using \"--datafieldURL\" option is empty.\n";
     317       }
     318     }
     319     $OptionsInfo{URLDataFieldLabel} = $DataFieldURLSplit[0];
     320     $OptionsInfo{URLCGIScriptName} = $DataFieldURLSplit[1];
     321     $OptionsInfo{URLParamName}  = $DataFieldURLSplit[2];
     322     $OptionsInfo{URLCmpdIdFieldName} = $DataFieldURLSplit[3];
     323   }
     324
     325 }
     326
     327 # Retrieve information about input SD files...
     328 sub RetrieveSDFilesInfo {
     329   my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot,  $OutFile, $DataFieldName);
     330
     331   %SDFilesInfo = ();
     332   @{$SDFilesInfo{FileOkay}} = ();
     333   @{$SDFilesInfo{OutFile}} = ();
     334
     335    FILELIST: for $Index (0 .. $#SDFilesList) {
     336     $SDFile = $SDFilesList[$Index];
     337
     338     $SDFilesInfo{FileOkay}[$Index] = 0;
     339     $SDFilesInfo{OutFile}[$Index] = '';
     340
     341     if (!(-e $SDFile)) {
     342       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     343       next FILELIST;
     344     }
     345     if (!CheckFileType($SDFile, "sd sdf")) {
     346       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     347       next FILELIST;
     348     }
     349     $FileDir = ""; $FileName = ""; $FileExt = "";
     350     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     351     if ($Options{root} && (@SDFilesList == 1)) {
     352       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
     353       if ($RootFileName && $RootFileExt) {
     354         $FileName = $RootFileName;
     355       }
     356       else {
     357         $FileName = $Options{root};
     358       }
     359       $OutFileRoot = $FileName;
     360     }
     361     else {
     362       $OutFileRoot = $FileName . "ModifiedDataFields";
     363     }
     364
     365     $OutFile = $OutFileRoot . ".$FileExt";
     366     if (lc($OutFile) eq lc($SDFile)) {
     367       warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
     368       next FILELIST;
     369     }
     370     if (!$Options{overwrite}) {
     371       if (-e $OutFile) {
     372         warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
     373         next FILELIST;
     374       }
     375     }
     376
     377     $SDFilesInfo{FileOkay}[$Index] = 1;
     378     $SDFilesInfo{OutFile}[$Index] = $OutFile;
     379   }
     380 }
     381
     382 # Setup script usage  and retrieve command line arguments specified using various options...
     383 sub SetupScriptUsage {
     384
     385   # Retrieve all the options...
     386   %Options = ();
     387   $Options{detail} = 1;
     388   $Options{keepolddatafields} = "none";
     389   $Options{mode} = "molname";
     390   $Options{molnamemode} = "labelprefix";
     391   $Options{molnamereplace} = "empty";
     392
     393   if (!GetOptions(\%Options, "detail|d=i", "datafieldscommon=s", "datafieldsmap=s", "datafieldsmapfile=s", "datafieldurl=s", "help|h", "keepolddatafields|k=s", "mode|m=s", "molname=s", "molnamemode=s", "molnamereplace=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
     394     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     395   }
     396   if ($Options{workingdir}) {
     397     if (! -d $Options{workingdir}) {
     398       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     399     }
     400     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     401   }
     402   if ($Options{keepolddatafields} !~ /^(all|unmappedonly|none)$/i) {
     403     die "Error: The value specified, $Options{keepolddatafields}, for option \"-k --keepolddatafields\" is not valid. Allowed values: all, unmappedonly, or none\n";
     404   }
     405   if ($Options{mode} !~ /^(molname|datafields|both)$/i) {
     406     die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: molname, datafields, or both\n";
     407   }
     408   if ($Options{molnamemode} !~ /^(datafield|labelprefix)$/i) {
     409     die "Error: The value specified, $Options{molnamemode}, for option \"--molnamemode\" is not valid. Allowed values: datafield or labelprefix\n";
     410   }
     411   if ($Options{molnamereplace} !~ /^(always|empty)$/i) {
     412     die "Error: The value specified, $Options{molnamereplace}, for option \"--molnamereplace\" is not valid. Allowed values: always or empty\n";
     413   }
     414   if (!IsPositiveInteger($Options{detail})) {
     415     die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
     416   }
     417 }
     418