#!/usr/bin/perl
#validtma.pl
use XML::Parser;
$opening = <<"EOF";

This script was created by Jules J. Berman on Jan 15, 2003.
The purpose of this script is to validate Tissue Microarray (TMA)
files that were created using the Common Data Elements (CDEs)
and sematics rules developed by the Association for Pathology
Informatics TMA Data Exchange Specification

This script requires the following two external Perl modules:
XML::Parser and MD5, both of which can be downloaded from
CPAN (Comprehensive Perl Archive Network) at www.cpan.org

The specification and all necessary URIs are listed and described
in a recently submitted manuscript.  All publications that refer
to or derive from the TMA Data Exchange Specification should
cite the following:

Berman JJ, Edgerton ME, Friedman B.  The Tissue Microarray Data
Exchange Specification: A Community-based, Open Source Tool for
Sharing Tissue Microarray Data. BMC Med Inform Decis Mak 2003,5.

This script may be used freely.  Bugs should be reported
to Jules Berman at bermanj\@mail.nih.gov

The software is provided "as is", without warranty of any kind,
express or implied, including but not limited to the warranties
of merchantability, fitness for a particular purpose and
noninfringement. in no event shall the authors or copyright
holders be liable for any claim, damages or other liability,
whether in an action of contract, tort or otherwise, arising
from, out of or in connection with the software or the use or
other dealings in the software.

Enter a file name you would like to validate.
The file must be in the same directory as the
validator script, validtma.pl and must end with the
extension .xml or .XML

The first part of the filename, prior to the extension
may not contain spaces and must be 8 characters
or less in length

Enter your filename now

EOF
print $opening;
my %index = &build_cde;
my $line = " ";
my $parser = XML::Parser->new( Handlers => {
  Init => \&handle_doc_start,
  Final => \&handle_doc_end,
  Start => \&handle_elem_start,
  End => \&handle_elem_end,
  Char => \&handle_char_data,
  });
my %filetags;
$file = <STDIN>;
$file =~ s/\n//;
if ($file eq "")
  {
  die "You didn't enter a filename.  Try again later.\n";
  }
$parser -> parsefile($file);

sub handle_doc_start
{
print "\nBegining to parse $file now\n\n";
}

sub handle_doc_end
{
exists($filetags{"header"})||die "No header tag. TMA file is invalid.\n";
exists($filetags{"tma"})||die "No tma tag. TMA file is invalid.\n";
exists($filetags{"histo"})||die "No histo tag. TMA file is invalid.\n";
exists($filetags{"slide"})||die "No slide tag. TMA file is invalid.\n";
exists($filetags{"core"})||die "No core tag. TMA file is invalid.\n";
exists($filetags{"block"})||die "No block tag. TMA file is invalid.\n";
print "\nFinished. $file is a valid Tissue Microarray File.\n"
}

my @build;
sub handle_elem_start
  {
  my $count = 0;
  my $previous;
  my ($expat, $name, %atts) = @_;
  $name =~ s/^[0-9a-z\-\_]*\://i;
  if (exists $index{$name})
    {
    $filetags{$name}++;
    print "$name\n";
    if ($name eq "histo")
      {
      if (scalar(@build) > 0)
        {
        die "Your first element must be the root element, histo\n";
        }
      undef @build;
      unshift (@build, $name)
      }
    if ($name eq "tma")
      {
      $previous = shift(@build);
      if ($previous ne "histo")
        {
        die "You have a tma element not preceded by a histo element\n";
        }
      else
        {
        unshift (@build, $name)
        }
      }
    if ($name eq "header")
      {
      $previous = shift(@build);
      if ($previous ne "tma")
        {
        die "You have a header element not preceded by a tma element\n";
        }
      else
        {
        unshift (@build, $name);
        }
      }
    if ($name eq "block")
      {
      $previous = shift(@build);
      if ($previous ne "header")
        {
        die "You have a block element not preceded by a header element\n";
        }
      else
        {
        unshift (@build, $name);
        }
      }
    if ($name eq "slide")
      {
      $previous = shift(@build);
      unshift(@build, $previous); #lets's put this back in the pile
      if (($previous eq "block") || ($previous eq "core")|| ($previous eq "slide"))
        {
        unshift (@build, $name);
        }
      else
        {
        die "You have a slide element not preceded by a block or core or slide element\n";
        }
      }
    if ($name eq "core")
      {
      $previous = shift(@build);
      unshift(@build, $previous);
      if (($previous eq "block") || ($previous eq "slide")|| ($previous eq "core"))
        {
        unshift (@build, $name);
        }
      else
        {
        die "You have a core element not preceded by a block or slide or core element\n";
        }
      }
    if ($name =~ /\_/)
      {
      my @name_array = split(/\_/, $name);
      my $last = pop(@name_array);
      my $next_to_last = pop(@name_array);
      $previous = shift (@build);
      if ($last eq $previous)
         {
         unshift (@build,$previous);  #The element has been repeated
         return;                      #That's ok.  Just put it back in the
         }                            #build array and return
      if ($previous eq $next_to_last)
         {
         unshift (@build, $previous); #the element has a new hierarchical
         unshift (@build, $last);     #extension.  add the previous last
         return;                      #and the new last to build array
         }                            #and return
      $previous = shift (@build);     #let's look back one more in build array
      if ($last eq $previous)
         {
         unshift (@build,$previous);  #The element has stepped back
         return;                      #one in the hierarchy. That's ok. Just put it back in the
         }                            #build array and return
      if ($previous eq $next_to_last)
         {
         unshift (@build, $previous); #the element has backed up one and
         unshift (@build, $last);     #added a new extensions.  Add the
         return;                      #previous and the last to the build array
         }                            #and return
      die "The element $name does not fit in the hierarchy\n";
      }
    }
  }

sub handle_elem_end
  {
  my($expat, $name) = @_;
  $name =~ s/^[0-9a-z\-\_]*\://i;
  if (exists $index{$name})
    {
    if ($name eq "tma")
      {
      undef @build;
      unshift(@build, $name)
      }
    if ($name =~ /\_/)
      {
      my @name_array = split(/\_/, $name);
      my $last = pop(@name_array);
      $previous = shift (@build);
      unless ($last eq $previous)
         {
         unshift (@build, $previous)
         }
       }
    }
  }

sub handle_char_data
  {
  my $expat = $_[0];
  $text .= "$_[1]";
  }


use MD5;
open (TEXT,"$file");
$context = new MD5;
$context->addfile(TEXT);
$digest = $context->digest();
$readable_digest = unpack ("H*", $digest);
print "\nThe one-way hash of your file is $readable_digest";

sub build_cde
{
my %build_index = qw(
histo 1
header 1
Title 1
Creator 1
SubjectandKeywords 1
Description 1
Publisher 1
Contributor 1
Date 1
ResourceType 1
Format 1
ResourceIdentifier 1
Source 1
Language 1
Relation 1
Coverage 1
RightsManagement 1
filename 1
tma 1
block 1
block_purpose 1
block_identifier 1
block_description 1
block_meshnumbers 1
block_related_blocks 1
block_creator 1
block_creation-date 1
block_protocol 1
block_number-of-cores 1
block_core-size 1
block_core-spacing 1
block_qa 1
block_status 1
block_array-hash 1
slide 1
slide_identifier 1
slide_cut-date 1
slide_storage 1
slide_section-thickness 1
slide_level 1
slide_sectioning-protocol 1
slide_test-date 1
slide_test-category 1
slide_test-protocol 1
slide_stain 1
slide_test-control 1
core 1
core_array-id 1
core_tissue-fixative 1
core_organism 1
core_demographics-record 1
core_anatomic-site 1
core_organ 1
core_tissue-origin 1
core_data-descriptor 1
core_data-descriptor_QC 1
core_clinical-info 1
core_clinical-info_id 1
core_clinical-info_availability 1
core_histo-repository 1
core_histo-repository_specimen-id 1
core_histo-repository_specimen-diagnosis 1
core_histo-repository_donor-block 1
core_histo-repository_donor-block_drill-site 1
core_histo-repository_donor-block_drill-site_diagnosis 1
core_results 1
core_results_slide-id 1
core_results_method-of-reading-data 1
core_results_number-of-nuclei-counted 1
core_results_tissue-intensity 1
core_results_percent-tissue-staining 1
core_results_compartment-staining 1
core_results_staining-pattern 1
core_image 1
core_image_slide-id 1
core_image_identifier 1
core_image_format 1
core_image_checksum 1
core_image_magnification 1
core_image_pixel_size 1);
return %build_index;
}
exit;