#!/usr/bin/perl

sub Get_SCDO_page_from_EBI {
  my ($Path, $owl) = @_;
  if (!open(OWL, "$Path/$owl")) {
    print "  !!! Could not open \"$owl\" file - program stopped !!!\n\n";
    exit(); }
  while (<OWL>) {
    chomp;
    if ($_ =~ /    \<\!\-\- http\:\/\/scdontology\.h3abionet\.org\/ontology\// && $_ =~ /SCDO/) {
      @array = split(/\//, $_);
      $array[4] =~ s/ \-\-\>//g;
      $cmd = "wget https://www.ebi.ac.uk/ols/ontologies/scdo/terms?iri=http://scdontology.h3abionet.org/ontology/$array[4]";
      system ($cmd);
      $cmd1 = "wget https://www.ebi.ac.uk/ols/ontologies/scdo/individuals?iri=http://scdontology.h3abionet.org/ontology/$array[4]";
      system ($cmd1);
      $cmd2 = "wget https://www.ebi.ac.uk/ols/ontologies/scdo/properties?iri=http://scdontology.h3abionet.org/ontology/$array[4]";
      system ($cmd2);
      
    }
  } close OWL;
}


sub Edit_SCDO_pages {
  my ($Path) = @_;
  @files = <*:*SCDO*>;
  foreach $file (@files) {
    if (!open(SCDO, "$file")) {
      print "  !!! Could not open \"$file\" file - program stopped !!!\n\n";
      exit(); }
    @array = split(/2F/, $file);
    open(OUT, ">$array[4]");
    print OUT '<!DOCTYPE html>
<html lang="en-US"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">

<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="profile" href="http://gmpg.org/xfn/11">
<link rel="pingback" href="http://scdontology.h3abionet.org/xmlrpc.php">

<title>SCDO_0000612</title>
<link rel="dns-prefetch" href="http://fonts.googleapis.com/">
<link rel="dns-prefetch" href="http://s.w.org/">
<link rel="alternate" type="application/rss+xml" title="Sickle Cell Disease Ontology Project » Feed" href="http://scdontology.h3abionet.org/index.php/feed/">
<link rel="alternate" type="application/rss+xml" title="Sickle Cell Disease Ontology Project » Comments Feed" href="http://scdontology.h3abionet.org/index.php/comments/feed/">
<link rel="alternate" type="text/calendar" title="Sickle Cell Disease Ontology Project » iCal Feed" href="http://scdontology.h3abionet.org/index.php/events/?ical=1">
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			<h1 class="entry-title">Sickle Cell Disease Ontology Project</h1>		</div>
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                <div class="grid_24 clearfix">
                    <div class="grid_24 clearfix">
                        <div class="grid_18 alpha">
                            <h1 property="name" style="margin: 0px;">Imaging Assay</h1>
                        </div>

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                                <div id="bloodhound" class="input-group">
                                    <input style="margin-bottom: 0.1em;" class="form-control typeahead" autofocus="autofocus" type="text" name="q" data-olswidget="select" data-olsontology="scdo" data-selectpath="../../" placeholder="Search SCDO" aria-describedby="basic-addon1" />

                                    <input type="hidden" name="ontology" value="scdo" />

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                        <a style="padding: 9px;border-bottom: none;" class="nounderline" target="blank" href="http://scdontology.h3abionet.org/ontology/SCDO_0000612"><img src="../../img/external_link.png" alt="^" title="Go to external page" /></a>
                        <span property="url" id="OLS_ID" style="font-size: small;color: grey;">http://scdontology.h3abionet.org/ontology/SCDO_0000612</span>
                        <p style="display:inline;"><button title="Copy id to clipboard" id="copyThis" data-clipboard-action="copy" data-clipboard-target="#OLS_ID" class="glyphicon glyphicon-copy" type="button"></button></p>

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                        <div property="description">

                            <!--@thymesVar id="definitionCitation" type="uk.ac.ebi.spot.ols.util.OBODefinitionCitation"-->

                            

                            <p>An assay that produces a picture of an entity.</p>
                        </div>

                        

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                </div>
            </section>

            <section>';
    while (<SCDO>) {
      chomp;
      if ($FLAG == 1) {
        
        if ($_ =~ /href/ && $_ =~ /SCDO/) {
          @record = split(/\"/, $_);
          @champ = split(/\=/, $record[1]);
          print OUT "$record[0]\"$champ[1]\"";
          for ($i=2; $i<=$#record-1; $i++) {
            print OUT "$record[$i]\""
          }
          print OUT "$record[$#record]\n";
        } else {
          print OUT "$_\n";
        }
      }
      if ($_ =~ /                \<div class\=\"grid\_24 clearfix\"\>/) {
        $FLAG = 1;
        print OUT "\n\n\n\n\n$_";
      }
      if ($FLAG == 1 && $_ =~ /^                \<\/div\>/) {
        $FLAG == 2;
      }
    } close SCDO;
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</body></html>';

  }
}

#Get_SCDO_page_from_EBI ("/home/ghedira/SCDO_EBI", "scdo.owl");
Edit_SCDO_pages ($Path);