#!/usr/bin/perl

## Version 1.0 ##
## Author: Christopher Villareal cvillareal@gmail.com ##
## Conventions
## $p_ is for a method/function parameter; $r_ is for a return value;
## p is for a pointer (ex. $pTwig); n for an integer; ph for a pointer to an HASH Table;
## pa for a pointer to an ARRAY; a for an ARRAY; h for an HASH
## ToDo: change over to using an sql database for dynamic generation ##
########################################################################################

## This script will take your xml file created by the vbi program and parse them into
## individual html files denoted by /$organism/ by BioobjectID or InteractionID
## for hyperlinking too by the curators with the master picture
## Put the picture into the w/e folder, but I would suggest something like
## /var/www/html/organism/index.html and then link by ../$bioobjID

## Modules ##
use strict;
use XML::Twig; # Handle the complicated handlers, and parse xml
use XML::Simple; # Use to insert parsed xml data into a html document
use DBI;
use CGI;
use Data::Dumper;
## End Modules ##

## Global Variables ## Some are necessary so their contents are available after subroutines##
my $pCGI = new CGI;
print $pCGI->header;
#my $organism = $pCGI->param('organism');
# my $sInput = $pCGI->param('input');
my $sAllBioObjectID;
my $sAllBRefs;
my $sAllBDesc;
my $sAllBFun;
my $sAllBName;
my $sAllBLoc;
my $sAllBType;
my $sAllIID;
my $sAllIRefs;
my $sAllICofac;
my $sAllIDesc;
my $sAllIType;
my %ref2pmid;
## End Global Variables ##

select(STDOUT); $| = 1; # make STDOUT unbuffered (so prints are done imediately)


my $parse = "RiftValleyFever_Pathway_pronet83.xml";

# Building the Twig Object and parse it using the insertCitations Method
my $pTwig = new XML::Twig('TwigRoots' => {'ProNet' => \&createHTML});

if( !defined($pTwig) )
{
  print "Err: Can't get XML::Twig Object !\n";
  exit -2;
}

$pTwig->parsefile($parse);

print "All done \:\) \n";

exit;

sub getBIOOB
{
  print "Grabbing all BioObject's Information \n";

  my $p_phXML = shift;

  my $paXMLBIOOB = getInfosFromXML($p_phXML, 'ProNet', 'BioObject');

## Creating all the arrays we're going to need
  my @aBioObjectID = ();
  my @aBRefs = ();
  my @aBDesc = ();
  my @aBName = ();
  my @aBType = ();
  my @aBLoc = ();
  my @aBFun = ();

## this foreach is pretty fun, its using the dumped data from $Var1 to then parse through and group what I want
## therefore, this can be extended to more functionality and even picture/hyperlink creations
## but I would suggest using a database if you were to do that and then you can have dynamic generation!
  foreach my $phBioObject (@{$paXMLBIOOB})
       {
       push @aBioObjectID, $phBioObject->{'BioObjectID'};

       push @aBRefs, $phBioObject->{'Refs'};

       push @aBDesc, $phBioObject->{'Description'};

       push @aBName, $phBioObject->{'Name'};

       push @aBType, $phBioObject->{'Type'};

       push @aBLoc, $phBioObject->{'Location'};

       push @aBFun, $phBioObject->{'Function'};
       }
## Now that I've grabbed everything, for this subroutine, I am going to finish it off by joining them all into a single
## placeholder than can then be foreached and split to make the htmls file lines
  $sAllBioObjectID = join('<<|>>', @aBioObjectID);

  $sAllBRefs = join('<<|>>', @aBRefs);

  $sAllBDesc = join('<<|>>', @aBDesc);

  $sAllBName = join('<<|>>', @aBName);

  $sAllBType = join('<<|>>', @aBType);

  $sAllBLoc = join('<<|>>', @aBLoc);

  $sAllBFun = join('<<|>>', @aBFun);

  print "Done grabbing all BioObject information\n";
}

sub getINTERACTIONS
{
  print "Grabbing all Interaction's Information\n";

  my $p_phXML = shift;

  my $paXMLINTERACTIONS = getInfosFromXML($p_phXML, 'ProNet', 'Interaction');

  my @aIID = ();
  my @aIRefs = ();
  my @aICofac = ();
  my @aIDesc = ();
  my @aIType = ();

  foreach my $phInteractions (@{$paXMLINTERACTIONS})

       {
       push @aIID, $phInteractions->{'InteractionID'};

       push @aIRefs, $phInteractions->{'Refs'};

       push @aICofac, $phInteractions->{'Co-factors'};

       push @aIDesc, $phInteractions->{'Description'};

       push @aIType, $phInteractions->{'Type'};

       }

  $sAllIID = join('<<|>>', @aIID);

  $sAllIRefs = join('<<|>>', @aIRefs);

  $sAllICofac = join('<<|>>', @aICofac);

  $sAllIDesc = join('<<|>>', @aIDesc);

  $sAllIType = join('<<|>>', @aIType);

  print "Done grabbing all interaction information\n";
}

sub getPMID
{
  my $p_phXML = shift;

  my $paXMLPMID = getInfosFromXML($p_phXML, 'ProNet', 'DataSource', 'JournalArticle');

  foreach my $phPMID (@{$paXMLPMID})
       {
       my $tempvar=$phPMID->{'PubMedID'};

       $ref2pmid{$phPMID->{'RefID'}}=$tempvar;

       }
  print Dumper(%ref2pmid);
}

sub getInfosFromXML
{
  my $p_phXML    = shift;
  my @p_aKeyList = @_;

  my $r_paXMLInfos;

  my $phTmpXML = $p_phXML;

  my @aKeyListSaved = @p_aKeyList;

  my $bReturnTmpXML = 1;

  foreach my $sKey (@p_aKeyList)
  {
     shift @aKeyListSaved;

     if( defined($phTmpXML) )
     {
        if( ref($phTmpXML) eq 'HASH' && defined($phTmpXML->{$sKey}) )
        {
           if( ref($phTmpXML->{$sKey}) eq 'HASH' )
           {
              $phTmpXML = $phTmpXML->{$sKey};
           }
           elsif( ref($phTmpXML->{$sKey}) eq 'ARRAY' )
           {
              foreach my $puTmp (@{$phTmpXML->{$sKey}})
              {
                 if( !defined($r_paXMLInfos) )
                 {
                    $r_paXMLInfos = [];
                 }

                 my $paXMLInfos = getInfosFromXML($puTmp, @aKeyListSaved);

                 if( defined($paXMLInfos) )
                 {
                    push @{$r_paXMLInfos}, @{$paXMLInfos};
                 }
              }
           }
           else
           {
              if( !defined($r_paXMLInfos) )
              {
                 $r_paXMLInfos = [];
              }

              push @{$r_paXMLInfos}, $phTmpXML->{$sKey};

              $bReturnTmpXML = 0;
              last;
           }
        }
        elsif( ref($phTmpXML) eq 'HASH' && !defined($phTmpXML->{$sKey}) )
        {
           $bReturnTmpXML = 0;
        }
     }
  }

  if( !defined($r_paXMLInfos) )
  {
     if( $bReturnTmpXML eq 1 )
     {
        $r_paXMLInfos = [$phTmpXML];
     }
     else
     {
        $r_paXMLInfos = [];
     }
  }

  return $r_paXMLInfos;

}

sub createHTML
{
  my $p_pTwig    = shift;
  my $p_pProNet  = shift;

  # Save XML ProNet into string
  my $sProNet = $p_pProNet->sprint;

  # release/purge Twig Datas (no more needed as we work on the $sProNet XML directly using XML::Simple
  $p_pTwig->purge;

  # Getting an XML::Simple Object from the ProNet XML (using sprint), which makes things simple to parse...
  my $pXS = new XML::Simple();

  my $phXML = eval{$pXS->XMLin($sProNet, 'forcearray' => 0)};

  if( $@ )
  {
     print "Err: $@\n";
     return;
  }

  if( !defined($phXML) )
  {
     return;
  }

# Call subroutines to call all the parsed information
  getBIOOB($phXML) || die "Could not get BioObjects";

  getINTERACTIONS($phXML) || die "Could not get InteractionObjects";

  getPMID($phXML) || die "Could not get citation information";

# Stuff those into new arrays after being simplified
# Check from HASH(xxxx) to NULL
  my @aAllBioObjectID = split ("<<|>>",$sAllBioObjectID);
  #my $nBioObjID;
  my @aAllBRefs = split ("<<|>>",$sAllBRefs);
  my $nBRefs;
#       <<|>>Odonnel<<|>>Grubman Frys<|>>
#       <JournalArticle RefID="Odonnell" PubMedID="15956593">
#       <<|>>15956593<<|>>15956593 1558648<<|>>
  my @aAllBDesc = split ("<<|>>",$sAllBDesc);
  #my $nBDesc;
  my @aAllBFun = split ("<<|>>",$sAllBFun);
  #my $nBFun;
  my @aAllBName = split ("<<|>>",$sAllBName);
  #my $nBName;
  my @aAllBLoc = split ("<<|>>",$sAllBLoc);
  #my $nBLoc;
  my @aAllBType = split ("<<|>>",$sAllBType);
  #my $nBType;
  my @aAllIID = split ("<<|>>",$sAllIID);
  #my $nIID;
  my @aAllIRefs = split ("<<|>>",$sAllIRefs);
  #my $nIRefs;
  my @aAllICofac = split ("<<|>>",$sAllICofac);
  #my $nICofac;
  my @aAllIDesc = split ("<<|>>",$sAllIDesc);
  #my $nIDesc;
  my @aAllIType = split ("<<|>>",$sAllIType);
  #my $nIType;

# let's create the webpages now
  print "Now creating all the html files needed in ... \n";

# Before using the script, make sure this points to the correct area
for (my $i=0;$i<@aAllBioObjectID; $i++) {
       # Change here to be able to tell the script where is should make the files too
       open (BIO,">/home/cvillareal/Desktop/kelly/RiftValleyFever/$aAllBioObjectID[$i].html") || die "Could not write Bio files!";
       print BIO "<html>";
       print BIO "<body>";
       print BIO "<p>Name: $aAllBName[$i]</p>";
       print BIO "<p>Type: $aAllBType[$i]</p>";
       print BIO "<p>Location: $aAllBLoc[$i]</p>";
       print BIO "<p>Fuction: $aAllBFun[$i]</p>";
       print BIO "<p>Description: $aAllBDesc[$i]</p>";
  foreach my $nRef(split (" ",$aAllBRefs[$i])){
       print BIO "<p><a href=\"http\:\/\/eutils\.ncbi\.nlm\.nih\.gov\/entrez\/eutils\/elink.fcgi\?dbfrom\=pubmed\&id\=$ref2pmid{$nRef}\&retmode\=ref\&cmd\=prlinks\">$nRef</a></p>";
       }
       print BIO "</body>";
       print BIO "</html>";
}

for (my $b=0;$b<@aAllIID; $b++) {
       open (INTER, ">/home/cvillareal/Desktop/kelly/RiftValleyFever/$aAllIID[$b].html") || "Could not write interaction files!";
       print INTER "<html>";
       print INTER "<body>";
       print INTER "<p>ID: $aAllIID[$b]</p>";
       print INTER "<p>Type: $aAllIType[$b]";
       print INTER "<p>Description: $aAllIDesc[$b]";
       print INTER "<p>CoFactors: $aAllICofac[$b]";
  foreach my $iRef(split (" ",$aAllIRefs[$b])){
       print INTER "<p><a href=\"http\:\/\/eutils\.ncbi\.nlm\.nih\.gov\/entrez\/eutils\/elink.fcgi\?dbfrom\=pubmed\&id\=$ref2pmid{$iRef}\&retmode\=ref\&cmd\=prlinks\">$iRef</a></p>";
       }
       print BIO "</body>";
       print BIO "</html>";
}