#!/usr/local/bin/perl 

###############################################################################
# Program     : ProcessProject.cgi
# Author      : Eric Deutsch <edeutsch@systemsbiology.org>
# $Id$
#
# Description : This CGI program that allows users to submit a processing
#		job to process a set of experiments in a project.
#
###############################################################################


###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
use lib qw (../../lib/perl);
use vars qw ($q $sbeams $sbeamsMA $dbh $current_contact_id $current_username
             $current_work_group_id $current_work_group_name
             $current_project_id $current_project_name
             $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
             $PK_COLUMN_NAME @MENU_OPTIONS $DEFAULT_COST_SCHEME);

use DBI;
#use CGI;
use CGI::Carp qw(fatalsToBrowser croak);
use POSIX;

use SBEAMS::Connection qw($q);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;

use SBEAMS::Microarray;
use SBEAMS::Microarray::Settings;
use SBEAMS::Microarray::Tables;

use lib "/net/arrays/Pipeline/tools/lib";

#$q = new CGI;
$sbeams = new SBEAMS::Connection;
$sbeamsMA = new SBEAMS::Microarray;
$sbeamsMA->setSBEAMS($sbeams);

###############################################################################
# Global Variables
###############################################################################
$TABLE_NAME = "MA_array_request";
$DEFAULT_COST_SCHEME = 1;
main();

###############################################################################
# Main Program:
#x
# Call $sbeams->InterfaceEntry with pointer to the subroutine to execute if
# the authentication succeeds.
###############################################################################
sub main { 

  #### Do the SBEAMS authentication and exit if a username is not returned
  exit unless ($current_username = $sbeams->Authenticate());

  #### Read in the default input parameters
  my %parameters;
  my $n_params_found = $sbeams->parse_input_parameters(q=>$q,parameters_ref=>\%parameters);
  #$sbeams->printDebuggingInfo($q);
  
  #### Process generic "state" parameters before we start
  $sbeams->processStandardParameters(parameters_ref=>\%parameters);

  #### Print the header, do what the program does, and print footer
  $sbeamsMA->printPageHeader();
  handle_request(parameters_ref=>\%parameters);
  $sbeamsMA->printPageFooter();


} # end main


###############################################################################
# handleRequest
#
# Test for specific form variables and process the request 
# based on what the user wants to do. 
###############################################################################
sub handle_request {
  my %args = @_;
  my $parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$parameters_ref};
  my $tab = $parameters{'tab'} || "main";
  $parameters{'project_id'} = $sbeams->getCurrent_project_id();
  $parameters{'username'} = $sbeams->getCurrent_username();

  ## Print standard page header
  $sbeams->printUserContext();

  #### Decide where to go based on form values
  if ($tab eq 'main') {

#	$sbeamsMA->printPageHeader();
  	print_start_screen(parameters_ref=>\%parameters);
#	$sbeamsMA->printPageFooter();

  }elsif ($tab eq 'arrayCount') {

#	$sbeamsMA->printPageHeader();
	print_array_request_screen(parameters_ref=>\%parameters);
#	$sbeamsMA->printPageFooter();

  }elsif ($tab eq 'arrayInfo') {

#	$sbeamsMA->printPageHeader();
	print_array_info_screen(parameters_ref=>\%parameters);
#	$sbeamsMA->printPageFooter();

  }elsif ($tab eq 'finalize') {

#	$sbeamsMA->printPageHeader();
	finalize(parameters_ref=>\%parameters);
#	$sbeamsMA->printPageFooter();

  }

} # end processRequests



###############################################################################
# Print Start Screen
###############################################################################
sub print_start_screen {
  my %args = @_;
  my $parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$parameters_ref};

  ## Standard Variables
  my $sql;
  my @rows;
  my $current_project = $parameters{'project_selector'} || $sbeams->getCurrent_project_id();
	

  print_start_screen_javascript();

  ## Print Introductory Header
  print qq~
  <H2><U>Welcome to the Microarray Data Entry Interface</U></H2>\n
  <BR>
     This tool is designed as a one-stop interface to recording information about your arrays.
  <BR>
  <FORM METHOD="POST" NAME="arrayProjectChooser"><BR>
  <INPUT TYPE="hidden" NAME="tab" VALUE="">
  $LINESEPARATOR
  <BR>
  <B>
  <FONT COLOR="red">
Step 1: Select Project<BR>
  </FONT>
  Into which project are these arrays going?
  </B>
  <A HREF="ManageTable.cgi?TABLE_NAME=project&ShowEntryForm=1">[Don\'t have a project? Click here to set one up]</A>
  <BR><BR>
  <SELECT NAME="projectSelector" onChange="prepareForSubmission()">
  <OPTION SELECTED VALUE="">--- SELECT FROM ACCESSIBLE PROJECTS ---
~;


  ## Previously, we used only $sbeams->getAccessibleProjects(), but this
  ## causes problems if the user doesn't have administrator access. Augmented
  ## with get_best_permission
  my $project_ids_list = join(',',$sbeams->getWritableProjects()) || '-1';

  $sql = qq~
    SELECT P.project_id, UL.username+' - '+P.name
      FROM $TB_PROJECT P 
      LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id = UL.contact_id )
     WHERE P.project_id IN ( $project_ids_list )
       AND P.record_status != 'D'
       AND UL.record_status != 'D'
     GROUP BY P.project_id, P.name, UL.username
     ORDER BY UL.username, P.name
	 ~;
  @rows = $sbeams->selectSeveralColumns($sql);

  foreach my $row_ref (@rows) {
	my ($project_id, $project_name) = @{$row_ref};
	print "  <OPTION VALUE=\"$project_id\">$project_name ($project_id)\n";
  }

  print qq~
  </SELECT>
  </FORM>
	~;
  return;
}

###############################################################################
# Print Start Screen Javascript
###############################################################################
sub print_start_screen_javascript {
	my $javascript = qq~
<SCRIPT LANGUAGE="Javascript">

function prepareForSubmission() {
  document.arrayProjectChooser.tab.value="arrayCount";
  document.arrayProjectChooser.submit();
}

</SCRIPT>		
			~;

	print $javascript;
}



###############################################################################
# Print Array Request Screen
###############################################################################
sub print_array_request_screen {
  my %args = @_;
  my $parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$parameters_ref};

  ## Standard Variables
  my $sql;
  my @rows;
  my $project = $parameters{'projectSelector'};
  my $contact_id = $sbeams->getCurrent_contact_id();
  print_array_request_javascript();

  # Create Slide Type Optionlist
  $sql = qq~
	SELECT slide_type_id, name+' (\$'+CONVERT(varchar(50),price)+')'
	  FROM $TBMA_SLIDE_TYPE
	 WHERE record_status != 'D'
	 ORDER BY name
	 ~;
  my $slide_optionlist = $sbeams->buildOptionList($sql);

  # Create Budget Optionlist
  $sql = qq~
	SELECT project_id, name + ' ['+budget+']' 
      FROM $TB_PROJECT 
     WHERE PI_contact_id='$contact_id' 
     ORDER BY name
	~;
  my $budget_optionlist = $sbeams->buildOptionList($sql);

  # Create Prep Optionlist
  $sql = qq~
	SELECT option_key, option_value
	  FROM $TBMA_ARRAY_REQUEST_OPTION
	 WHERE option_type = 'hybridization_request'
	 ORDER BY sort_order
	 ~;

  my $prep_optionlist = $sbeams->buildOptionList($sql);
  

  # Create Analysis Optionlist
  $sql = qq~
	SELECT option_key, option_value+' (\$'+CONVERT(varchar(50),price)+')'
	  FROM $TBMA_ARRAY_REQUEST_OPTION
	 WHERE option_type = 'scanning_request'
	 ORDER BY sort_order
	 ~;

  my $analysis_optionlist = $sbeams->buildOptionList($sql);

  
  ## Print Introductory Header
  print qq~
  <H2><U>Microarray Data Entry Interface</U></H2>\n
  <FORM METHOD="POST" NAME="arrayCount"><BR>
  <INPUT TYPE="hidden" NAME="tab">
  <INPUT TYPE="hidden" NAME="projectSelector" VALUE="$project">
  $LINESEPARATOR
  <BR>
  <B>
  <FONT COLOR="red">
Step 2: Select \# of Arrays<BR>
  </FONT>
  <TABLE>
  <TR>
   <TD>How many arrays will you be submitting today?&nbsp;&nbsp;</TD>
   <TD><INPUT TYPE="text" NAME="arrayNumber" SIZE="3"MAXLENGTH="3"></TD>
  </TR>
  <TR>
   <TD>On what budget are these being paid?</TD>
   <TD><SELECT NAME="budget">
       <OPTION SELECT VAVLUE="-1">--- SELECT BUDGET ---
       $budget_optionlist
       </SELECT></TD>
  </TR>
  <TR>
   <TD>What type of arrays are these?</TD>
   <TD><SELECT NAME="arrayType">
       <OPTION SELECTED VALUE="-1">--- SELECT SLIDE TYPE ---
       $slide_optionlist
       </SELECT></TD>
  </TR>
  <TR>
   <TD>What was the requests prep?</TD>
   <TD><SELECT NAME="prepType">
       <OPTION SELECT VALUE="-1">--- SELECT PREP TYPE ---
       $prep_optionlist
       </SELECT></TD>
  </TR>
  <TR>
   <TD>What was the requested analysis?</TD>
   <TD><SELECT NAME="analysisType">
       <OPTION SELECT VALUE="-1">--- SELECT ANALYSIS TYPE ---
       $analysis_optionlist
       </SELECT></TD>
  </TR>
  </TABLE>
  <INPUT TYPE="button" NAME="nextButton" VALUE="Next-->" onClick="prepareForSubmission()">
  </B>

  <BR><BR>

  </FORM>
	~;
  return;
}

###############################################################################
# Print Array Request Javascript
###############################################################################
sub print_array_request_javascript {
  my $javascript = qq~
<SCRIPT LANGUAGE="Javascript">

function prepareForSubmission() {
  var isNum = verifyNumber();
  if (isNum == -1) {return;}
  if (document.arrayCount.arrayType.value < 0) {
	alert("Please Select Slide Type");
	return;
  }
  if (document.arrayCount.budget.value < 0) {
	alert("Please Select Budget");
	return;
  }  if (document.arrayCount.prepType.value < 0) {
	alert("Please Select Prep Type");
	return;
  }  if (document.arrayCount.analysisType.value < 0) {
	alert("Please Select Analysis Type");
	return;
  }
  document.arrayCount.tab.value="arrayInfo";
  document.arrayCount.submit();
}


function verifyNumber(){
  //need just an integer
  var location = document.arrayCount.arrayNumber;
  var testValue = location.value;
  var number = parseInt(testValue);
  if(isNaN(number) || number < 0){
	alert(testValue+" is not valid");
	location.value ="";
	return -1;
  }else {
	return 0;
  }
}//end verifyNumber

</SCRIPT>		
			~;

  print $javascript;
}

###############################################################################
# Print Array Info Screen
###############################################################################
sub print_array_info_screen {
  my %args = @_;
  my $parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$parameters_ref};

  ## Standard Variables
  my $sql;
  my @rows;
  my $array_count = $parameters{'arrayNumber'};
  my $successful = 1;
  my $status_report = "";

  ## Hash of array layouts 

  # Determine the organism
  $sql = qq~
	SELECT O.organism_name
	  FROM $TB_ORGANISM O
	  LEFT JOIN $TBMA_SLIDE_TYPE S ON (S.organism_id = O.organism_id)
	 WHERE S.slide_type_id = $parameters{'arrayType'}
	   AND S.record_status != 'D'
	   ~;
  @rows = $sbeams->selectOneColumn($sql);
  my $organism = $rows[0];
  $organism =~ tr /A-Z/a-z/;
  
  ###############################
  ## SPECIAL ORGANISM HANDLING ##
  ###############################
  if ($organism eq "halobacterium") {
	$organism = "halo";
  }
  
  $sql = qq~
	SELECT layout_id, name
	  FROM $TBMA_ARRAY_LAYOUT
	 WHERE name LIKE '$organism%'
	 ~;
  @rows = $sbeams->selectSeveralColumns($sql);

  my %array_layouts;
  foreach my $row (@rows) {
	my ($layout_id, $array_name) = @{$row};
	$array_name =~ /.*\_(\d+)-(\d+)/;
	my $low_val = $1;
	my $hi_val = $2;
	$array_layouts{$low_val,$hi_val} = $layout_id;
  }

  ## Hash of printing batches
  $sql = qq~
	SELECT slide_list, printing_batch_id
	FROM $TBMA_PRINTING_BATCH 
	WHERE slide_type_id = $parameters{'arrayType'}
	AND record_status != 'D'
	~;
  my %printing_batches = $sbeams->selectTwoColumnHash($sql);


  ## Create Labeling Optionlist
  $sql = qq~
	SELECT labeling_method_id,name
	  FROM $TBMA_LABELING_METHOD
	 ORDER BY sort_order,name
	 ~;
  my $optionlist=$sbeams->buildOptionList($sql);


  ## Create Labeling Protocol Optionlist
  $sql = qq~
SELECT P.protocol_id, P.name
  FROM $TB_PROTOCOL P
  LEFT JOIN $TB_PROTOCOL_TYPE PT ON (PT.protocol_type_id = P.protocol_type_id)
 WHERE PT.name IN ('extract_labeling', 'Genicon Labeling')
 ~;
  my $labeling_optionlist=$sbeams->buildOptionList($sql);
 

  ## Create Hybridization Protocol Optionlist
  $sql = qq~
SELECT P.protocol_id, P.name
  FROM $TB_PROTOCOL P
  LEFT JOIN protocol_type PT ON (PT.protocol_type_id = P.protocol_type_id)
 WHERE PT.name = 'hybridization'
 ~;
  my $hybridization_optionlist = $sbeams->buildOptionList($sql);


  ## Create Scanning Protocol Optionlist
  $sql = qq~
SELECT P.protocol_id, P.name
  FROM $TB_PROTOCOL P
  LEFT JOIN protocol_type PT ON (PT.protocol_type_id = P.protocol_type_id)
 WHERE PT.name = 'array_scanning'
 ~;
  my $scanning_optionlist = $sbeams->buildOptionList($sql);


  ## Create Quantitation Protocol Optionlist
  $sql = qq~
SELECT P.protocol_id, P.name
  FROM $TB_PROTOCOL P
  LEFT JOIN protocol_type PT ON (PT.protocol_type_id = P.protocol_type_id)
 WHERE PT.name = 'image_analysis'
 ~;
  my $spotfinding_optionlist = $sbeams->buildOptionList($sql);
  

  ## Array ID optionlist
  # 1) Gather all possible slides that have been created in the past year
  # 2) See if they have an appropriate array_layout and printing_batch
  # 3) make an optionlist of resultset

  # All possible slides that have been made in the past 12 months
  $sql = qq~
SELECT S.slide_id, slide_number
  FROM $TBMA_SLIDE S 
  LEFT JOIN $TBMA_ARRAY A ON ( S.slide_id=A.slide_id ) 
 WHERE A.slide_id IS NULL
   AND DATEDIFF(MONTH,S.date_created,GETDATE()) < 24
 ORDER BY slide_number
 ~;
  @rows = $sbeams->selectSeveralColumns($sql);

  # Verify that slides have a valid array_layout and printing batch
  my @valid_arrays;
  foreach my $slide_ref (@rows) {
	my $found_array_layouts = 0;
	my $found_printing_batches = 0;
	my ($slide_id, $slide_number) = @{$slide_ref};

	foreach my $key (keys %array_layouts){
	  my @temp = split /\W/,$key;
	  my $low_val = $temp[0];
	  my $hi_val = $temp[1];
	  if ($low_val <= $slide_number && $hi_val >= $slide_number) {
		$found_array_layouts++;
	  }
	}
	if ($found_array_layouts > 1) {
	  $status_report .= "WARNING: Slide \#$slide_number has multiple array layouts associated with it.  Contact the Array Core if you are planning on using this!<BR> \n";
	}

	foreach my $key (keys %printing_batches) {
	  my @temp = split /-/, $key;
	  my $low_val = $temp[0];
	  my $hi_val = $temp[1];
	  if ($low_val <= $slide_number && $hi_val >= $slide_number) {
		$found_printing_batches++;
	  }
	}
	if ($found_printing_batches > 1) {
	  $status_report .= "WARNING: Slide \#$slide_number has multiple printing batches associated with it.  Contact the Array Core if you are planning on using this slide!<BR>\n";
	}

	if ($found_printing_batches == 1 && $found_array_layouts == 1) {
	  push @valid_arrays, $slide_id;
	}
  }

  my $array_ids = join ',', @valid_arrays;
  # make optionlist
  $sql = qq~
SELECT slide_number, slide_number
  FROM $TBMA_SLIDE S 
  LEFT JOIN $TBMA_ARRAY A ON ( S.slide_id=A.slide_id ) 
 WHERE A.slide_id IS NULL
   AND DATEDIFF(MONTH,S.date_created,GETDATE()) < 24
   AND S.slide_id IN ( $array_ids )
 ORDER BY slide_number
 ~;
  my $array_optionlist = $sbeams->buildOptionList($sql);


  ## Print Introductory Header
  print qq~
  <H2><U>Microarray Data Entry Interface</U></H2>\n
  <FORM METHOD="POST" NAME="arrayInfo"><BR>
  <INPUT TYPE="hidden" NAME="tab">
  <INPUT TYPE="hidden" NAME="project" VALUE="$parameters{'projectSelector'}">
  <INPUT TYPE="hidden" NAME="arrayNumber" VALUE="$parameters{'arrayNumber'}">
  <INPUT TYPE="hidden" NAME="slideType" VALUE="$parameters{'arrayType'}">
  <INPUT TYPE="hidden" NAME="analysisType" VALUE="$parameters{'analysisType'}">
  <INPUT TYPE="hidden" NAME="prepType" VALUE="$parameters{'prepType'}">
  <INPUT TYPE="hidden" NAME="budget" VALUE="$parameters{'budget'}">
  $LINESEPARATOR
  <BR>
  <B>
  <FONT COLOR="red">
Step 3: Array Information<BR>
  </FONT>
  </B>
  <BR>
  $status_report<BR>
  <TABLE BORDER>
  <TR BGCOLOR="#1C3887">
   <TD><FONT COLOR="white">Array ID</FONT></TD>
   <TD><FONT COLOR="white">Sample \#1 Name</FONT></TD>
   <TD><FONT COLOR="white">Sample \#1 Label</FONT></TD>
   <TD><FONT COLOR="white">Dye Lot \#</FONT></TD>
   <TD><FONT COLOR="white">Sample \#2 Name</FONT></TD>
   <TD><FONT COLOR="white">Sample \#2 Label</FONT></TD>
   <TD><FONT COLOR="white">Dye Lot \#</FONT></TD>
   <TD><FONT COLOR="white">Labeling Protocol</FONT></TD>
   <TD><FONT COLOR="white">Date Labeled (YYYY-MM-DD)</FONT></TD>
   <TD><FONT COLOR="white">Hybridization Protocol</FONT></TD>
   <TD><FONT COLOR="white">Date Hybridized(YYYY-MM-DD)</FONT></TD>
   <TD><FONT COLOR="white">Scanning Protocol</FONT></TD>
   <TD><FONT COLOR="white">Scan Date(YYYY-MM-DD)</FONT></TD>
   <TD><FONT COLOR="white">Scan Data Flag</FONT></TD>
   <TD><FONT COLOR="white">Image Location</FONT></TD>
   <TD><FONT COLOR="white">Quantitation Protocol</FONT></TD>
   <TD><FONT COLOR="white">Quantitation Date(YYYY-MM-DD)</FONT></TD>
   <TD><FONT COLOR="white">Quantitation Data Flag</FONT></TD>
   <TD><FONT COLOR="white">Quantitation File Location</FONT></TD>
  </TR>
  <TR BGCOLOR="#1C3887">
   <TD><!-- Array ID --></TD>
   <TD><INPUT TYPE="TEXT" NAME="sample0checked" VALUE="- Set Checked To -" onFocus="blank(this)">
       <INPUT TYPE="button" VALUE="Apply" onClick="Javascript:setChecked(0);"></TD>
   <TD><SELECT NAME="sample0labmeth_all" onChange="Javascript:setAllMethods(0);">
   <OPTION VALUE="-1">--- SET ALL LABELING METHODS TO: ---
   $optionlist;
   </SELECT>
   <TD><!-- Sample 1 Dye Lot --></TD>
   <TD><INPUT TYPE="TEXT" NAME="sample1checked" VALUE="- Set Checked To -"onFocus="blank(this)">
       <INPUT TYPE="button" VALUE="Apply" onClick="Javascript:setChecked(1);"></TD>
   <TD><SELECT NAME="sample1labmeth_all" onChange="Javascript:setAllMethods(1);">
   <OPTION VALUE="-1">--- SET ALL LABELING METHODS TO: ---
   $optionlist;
   </SELECT></TD>
   <TD><!-- Sample 2 Dye Lot --></TD>
   <TD><SELECT NAME="labprot_all" onChange="Javascript:setAllMethods(2);">
   <OPTION VALUE="-1">--- SET ALL LABELING PROTOCOLS TO: ---
   $labeling_optionlist;
   </SELECT></TD>
   <TD ALIGN="CENTER"><INPUT TYPE="button" VALUE="Set to Now" onClick="Javascript:clickedNow('lab');"></TD>
   <TD><SELECT NAME="hybprot_all" onChange="Javascript:setAllMethods(3);">
   <OPTION VALUE="-1">--- SET ALL HYBRIDIZATION PROTOCOLS TO: ---
   $hybridization_optionlist;
   </SELECT></TD>
   <TD ALIGN="CENTER"><INPUT TYPE="button" VALUE="Set to Now" onClick="Javascript:clickedNow('hyb');"></TD>
   <TD><SELECT NAME="scanprot_all" onChange="Javascript:setAllMethods(4);">
   <OPTION VALUE="-1">--- SET ALL SCANNING PROTOCOLS TO: ---
   $scanning_optionlist;
   </SELECT></TD>
   <TD ALIGN="CENTER"><INPUT TYPE="button" VALUE="Set to Now" onClick="Javascript:clickedNow('scan');"></TD>
   <TD><SELECT NAME="scanflag_all" onChange="Javascript:setAllMethods(5);">
   <OPTION VALUE="-1">--- SET ALL DATA FLAGS TO: ---
   <OPTION VALUE="OK">OK
   <OPTION VALUE="BAD">BAD
   </SELECT></TD>
   <TD><!-- Image Location --></TD>
   <TD><SELECT NAME="quantprot_all" onChange="Javascript:setAllMethods(6);">
   <OPTION VALUE="-1">--- SET ALL SPOTFINDING PROTOCOLS TO: ---
   $spotfinding_optionlist;
   </SELECT></TD>
   <TD ALIGN="CENTER"><INPUT TYPE="button" VALUE="Set to Now" onClick="Javascript:clickedNow('quant');"></TD>
   <TD><SELECT NAME="quantflag_all" onChange="Javascript:setAllMethods(7);">
   <OPTION VALUE="-1">--- SET ALL DATA FLAGS TO: ---
   <OPTION VALUE="OK">OK
   <OPTION VALUE="BAD">BAD
   </SELECT></TD>
   <TD></TD>	 
  </TR>
  ~;
  for (my $m=0;$m<$array_count;$m++) {
	print qq~
  <TR BGCOLOR="#CCFFFF">
   <TD><SELECT NAME="array_$m" onChange="setLocations(this.value,document.arrayInfo.quantprot_$m.value, document.arrayInfo.quantfile_$m,document.arrayInfo.scanfile_$m)">
       <OPTION VALUE="-1" SELECTED>
	   $array_optionlist
	   </SELECT></TD>
   <TD><NOBR><INPUT TYPE="checkbox" NAME="sample0check_$m">
             <INPUT TYPE="text" NAME="sample0name_$m" SIZE="25" MAXLENGTH="255"></NOBR></TD>
   <TD><SELECT NAME="sample0labmeth_$m">
       <OPTION VALUE="-1" SELECTED>
	   $optionlist
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="sample0dye_$m" SIZE="6" MAXLENGTH="20"></TD>
   <TD><NOBR><INPUT TYPE="checkbox" NAME="sample1check_$m">
             <INPUT TYPE="text" NAME="sample1name_$m" SIZE="25" MAXLENGTH="255"></NOBR></TD>
   <TD><SELECT NAME="sample1labmeth_$m">
       <OPTION VALUE="-1" SELECTED>
	   $optionlist
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="sample1dye_$m" SIZE="6" MAXLENGTH="20"></TD>
   <TD><SELECT NAME="labprot_$m">
       <OPTION VALUE="-1" SELECTED>
	   $labeling_optionlist
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="labdate_$m" SIZE="25"></TD>	   
   <TD><SELECT NAME="hybprot_$m">
       <OPTION VALUE="-1" SELECTED>
       $hybridization_optionlist
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="hybdate_$m" SIZE="25"></TD>
   <TD><SELECT NAME="scanprot_$m">
       <OPTION VALUE="-1" SELECTED>
       $scanning_optionlist
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="scandate_$m" SIZE="25"></TD>
   <TD><SELECT NAME="scanflag_$m">
       <OPTION VALUE="-1" SELECTED>
       <OPTION VALUE="OK">OK
	   <OPTION VALUE="BAD">BAD
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="scanfile_$m" SIZE="50"></TD>
   <TD><SELECT NAME="quantprot_$m">
       <OPTION VALUE="-1" SELECTED>
       $spotfinding_optionlist
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="quantdate_$m" SIZE="25"></TD>
   <TD><SELECT NAME="quantflag_$m">
       <OPTION VALUE="-1" SELECTED>
       <OPTION VALUE="OK">OK
	   <OPTION VALUE="BAD">BAD
	   </SELECT></TD>
   <TD><INPUT TYPE="text" NAME="quantfile_$m" SIZE = "50"></TD>
  </TR>
  ~;
  }
print qq~
  </TABLE>
  <INPUT TYPE="button" NAME="nextButton" VALUE="Done!" onClick="prepareForSubmission();">
  <BR><BR>
  </FORM>
	~;

  print_array_info_javascript($array_count);
  

  return;
}

###############################################################################
# Print Array Info Javascript
###############################################################################
sub print_array_info_javascript {
  my $array_requests = shift @_;
  my $javascript = qq~
<SCRIPT LANGUAGE="Javascript">
    ~;

  my $samples = 2;
  for (my $m=0;$m<$samples;$m++) {
	$javascript .= "var sample".$m."_array = new Array($array_requests);\n";
	$javascript .= "var check".$m."_array = new Array($array_requests);\n";
	$javascript .= "var name".$m."_array = new Array($array_requests);\n";
  }

  $javascript .= "var labprot_array = new Array($array_requests);\n";
  $javascript .= "var hybprot_array = new Array($array_requests);\n";
  $javascript .= "var scanprot_array = new Array($array_requests);\n";
  $javascript .= "var quantprot_array = new Array($array_requests);\n";
  $javascript .= "var scanflag_array = new Array($array_requests);\n";
  $javascript .= "var quantflag_array = new Array($array_requests);\n";
  $javascript .= "var labdate_array = new Array($array_requests);\n";
  $javascript .= "var hybdate_array = new Array($array_requests);\n";
  $javascript .= "var scandate_array = new Array($array_requests);\n";
  $javascript .= "var quantdate_array = new Array($array_requests);\n";

  for (my $i=0;$i<$array_requests;$i++) {
	$javascript .= "labprot_array[".$i."] = document.arrayInfo.labprot_".$i.";\n";
	$javascript .= "hybprot_array[".$i."] = document.arrayInfo.hybprot_".$i.";\n";
	$javascript .= "scanprot_array[".$i."] = document.arrayInfo.scanprot_".$i.";\n";
	$javascript .= "quantprot_array[".$i."] = document.arrayInfo.quantprot_".$i.";\n";
	$javascript .= "scanflag_array[".$i."] = document.arrayInfo.scanflag_".$i.";\n";
	$javascript .= "quantflag_array[".$i."] = document.arrayInfo.quantflag_".$i.";\n";
	$javascript .= "labdate_array[".$i."] = document.arrayInfo.labdate_".$i.";\n";
	$javascript .= "hybdate_array[".$i."] = document.arrayInfo.hybdate_".$i.";\n";
	$javascript .= "scandate_array[".$i."] = document.arrayInfo.scandate_".$i.";\n";
	$javascript .= "quantdate_array[".$i."] = document.arrayInfo.quantdate_".$i.";\n";
	for (my $j=0;$j<$samples;$j++) {
	  $javascript .= "sample".$j."_array[".$i."] = document.arrayInfo.sample".$j."labmeth_".$i.";\n";
	  $javascript .= "check".$j."_array[".$i."] = document.arrayInfo.sample".$j."check_".$i.";\n";
	  $javascript .= "name".$j."_array[".$i."] = document.arrayInfo.sample".$j."name_".$i.";\n";
	}
  }

  $javascript .= qq~

function blank(location) {
  location.value = "";
}

function setChecked(sample_ID) {
  var template;
  if (sample_ID == 0) {
	template = document.arrayInfo.sample0checked.value;
	for (var n=0;n<check0_array.length;n++) {
	  if (check0_array[n].checked){
		name0_array[n].value = template;
	  }
	  check0_array[n].checked = false;
	}
	document.arrayInfo.sample0checked.value = "- Set Checked To -";
  }else if (sample_ID == 1){
	template = document.arrayInfo.sample1checked.value;
	for (var n=0;n<check1_array.length;n++) {
	  if (check1_array[n].checked) {
		name1_array[n].value = template;
	  }
	  check1_array[n].checked = false;
	}
	document.arrayInfo.sample1checked.value = "- Set Checked To -";
  }
}

function clickedNow(id) {
  today = new Date();
  date_value =
      today.getFullYear() + "-" + (today.getMonth()+1) + "-" +
      today.getDate() + " " +
      today.getHours() + ":" +today.getMinutes();


  if (id == "quant") {
	for (var n=0; n<quantdate_array.length;n++){
	  quantdate_array[n].value=date_value;
    }
  }
  if (id == "scan") {
	for (var n=0; n<scandate_array.length;n++){
	  scandate_array[n].value=date_value;
    }
  }
  if (id == "hyb") {
	for (var n=0; n<hybdate_array.length;n++){
	  hybdate_array[n].value=date_value;
    }
  }
  if (id == "lab") {
	for (var n=0; n<labdate_array.length;n++){
	  labdate_array[n].value=date_value;
    }
  }
  return;
}

function setAllMethods(id){
  if (id == 0){
    for (var n=0; n<sample0_array.length;n++){
	sample0_array[n].options[document.arrayInfo.sample0labmeth_all.selectedIndex].selected=true;
    }
	document.arrayInfo.sample0labmeth_all.selectedIndex = 0;
  }
  if (id == 1){
    for (var n=0; n<sample1_array.length;n++){
	sample1_array[n].options[document.arrayInfo.sample1labmeth_all.selectedIndex].selected=true;
    }
	document.arrayInfo.sample1labmeth_all.selectedIndex = 0;
  }
  if (id == 2){
    for (var n=0; n<labprot_array.length;n++){
	labprot_array[n].options[document.arrayInfo.labprot_all.selectedIndex].selected=true;
    }
	document.arrayInfo.labprot_all.selectedIndex = 0;
  }
  if (id == 3){
    for (var n=0; n<hybprot_array.length;n++){
	hybprot_array[n].options[document.arrayInfo.hybprot_all.selectedIndex].selected=true;
    }
	document.arrayInfo.hybprot_all.selectedIndex = 0;
  }
  if (id == 4){
    for (var n=0; n<scanprot_array.length;n++){
	scanprot_array[n].options[document.arrayInfo.scanprot_all.selectedIndex].selected=true;
    }
	document.arrayInfo.scanprot_all.selectedIndex = 0;
  }
  if (id == 5){
    for (var n=0; n<scanflag_array.length;n++){
	scanflag_array[n].options[document.arrayInfo.scanflag_all.selectedIndex].selected=true;
    }
	document.arrayInfo.scanflag_all.selectedIndex = 0;
  }
  if (id == 6){
    for (var n=0; n<quantprot_array.length;n++){
	quantprot_array[n].options[document.arrayInfo.quantprot_all.selectedIndex].selected=true;
    }
	document.arrayInfo.quantprot_all.selectedIndex = 0;
  }
  if (id == 7){
    for (var n=0; n<quantflag_array.length;n++){
	quantflag_array[n].options[document.arrayInfo.quantflag_all.selectedIndex].selected=true;
    }
	document.arrayInfo.quantflag_all.selectedIndex = 0;
  }
}

function prepareForSubmission() {
  document.arrayInfo.tab.value="finalize";
  document.arrayInfo.submit();
}

function verifyNumber(){
  //need just an integer
  var location = document.arrayInfo.arrayNumber;
  var testValue = location.value;
  var number = parseInt(testValue);
  if(isNaN(number) || number < 0){
	alert(testValue+" is not valid");
	location.value ="";
	return -1;
  }else {
	return 0;
  }
}//end verifyNumber

function setLocations (array_name, protocol_name, QALocation, scanLocation) {
  setImageLocation(array_name, scanLocation);
  setQALocation(array_name, protocol_name, QALocation);
  return;
}

function setImageLocation(array_name, scanLocation) {
    if (array_name.substr(array_name.length-9,99) == " - *DONE*") {
      array_name = array_name.substr(0,array_name.length-9);
    }

    serial_number = array_name;
    if (serial_number.substr(serial_number.length-1,99) >= "A") {
      serial_number = serial_number.substr(0,array_name.length-1);
    }

    today = new Date();
    date_value =
	"" + today.getFullYear() +
	addLeadingZeros((today.getMonth()+1),2) +
	addLeadingZeros(today.getDate(),2)
	date_value = date_value.substr(2,6);

    start_group = Math.round(serial_number/100-0.5)*100+1;
    start_group = addLeadingZeros(start_group.toString(),5);

    end_group = Math.round(serial_number/100+0.5)*100;
    end_group = addLeadingZeros(end_group.toString(),5);

    array_name = addLeadingZeros(array_name.toString(),5);

    scanLocation.value =
	"/net/arrays/ScanArray_Images/" +
	start_group + "-"+ end_group + "/" +
	array_name + "_" + date_value;
    return;
}

function addLeadingZeros(instring,ndigits) {
  instring = instring.toString();
  while (instring.length < ndigits) { instring = "0" + instring; }
  return instring;
}

function setQALocation(array_name, protocol_name, QALocation) {
  array_name = array_name.toString();

  //Shouldn\'t need, but keep as a safety measure anyway
  if (array_name.substr(array_name.length-9,99) == " - *DONE*") {
    array_name = array_name.substr(0,array_name.length-9);
  }
  array_name = addLeadingZeros(array_name,5);

  start_group = Math.round(array_name/100-0.5)*100+1;
  start_group = addLeadingZeros(start_group.toString(),5);

  end_group = Math.round(array_name/100+0.5)*100;
  end_group = addLeadingZeros(end_group.toString(),5);

  protocol_name = protocol_name.toString();
  extension = ".csv";
  
  if (protocol_name.search(/QuantArray/i)>-1) { extension = ".qa"; }
  if (protocol_name.search(/Dapple/i)>-1) { extension = ".dapple"; }

  QALocation.value =
      "/net/arrays/Quantitation/" +
      start_group + "-"+ end_group + "/" +
      array_name + extension;

  return;
}
</SCRIPT>	   
			~;

  print $javascript;
}




###############################################################################
# finalize
# NOTE: the 'array_name' field within microarray.dbo.array is named
#       the same as the 'slide_number' field in microarray.dbo.slide.
#       Also, the page is hinged upon the standardized naming of print
#       batches.  We can intuit the print batch based upon slide number
#       and organism (from slide type).  However, if the naming convention is 
#       different, this won't work!!
###############################################################################
sub finalize {
  my %args = @_;
  my $parameters_ref = $args{'parameters_ref'};
  my %parameters = %{$parameters_ref};
  
  ## Standard Variables
  my $sql;
  my @rows;
  my $contact_id = $sbeams->getCurrent_contact_id();

  ## Other Variables
  my $project = $parameters{'project'};
  my $cost_scheme_id = $DEFAULT_COST_SCHEME unless ( $parameters{'cost_scheme_id'} >= 1 );
  my $successful = 1;  
  my $error_messages ="";
  my $slide_type_id = $parameters{'slideType'};
  my $analysis_type = $parameters{'analysisType'};
  my %array_info;
  

  ## Determine Number of arrays
  my $array_count = $parameters{'arrayNumber'};


  ## Print Introductory Header
  print qq~
  <H2><U>Welcome to the Microarray Data Entry Interface</U></H2>\n
  <BR>
     This tool is designed as a one-stop interface to recording information about your arrays.
  <BR>
  <FORM METHOD="POST" NAME="arrayProjectChooser"><BR>
  <INPUT TYPE="hidden" NAME="tab" VALUE="">
  $LINESEPARATOR
  <BR>
  ~;


  ######################################################################################
  # Verify that we won't have any problems INSERTing the records.                      #
  # Intuit print batch and array layout.  SKETCHY!  Is there a cleaner way to do this? #
  ######################################################################################

  # Determine the organism
  $sql = qq~
	SELECT O.organism_name
	  FROM $TB_ORGANISM O
	  LEFT JOIN $TBMA_SLIDE_TYPE S ON (S.organism_id = O.organism_id)
	 WHERE S.slide_type_id = $slide_type_id
	   AND S.record_status != 'D'
	   ~;
  @rows = $sbeams->selectOneColumn($sql);
  my $organism = $rows[0];
  $organism =~ tr /A-Z/a-z/;
  
  ###############################
  ## SPECIAL ORGANISM HANDLING ##
  ###############################
  if ($organism eq "halobacterium") {
	$organism = "halo";
  }
  
  ## Determine array_layout information
  $sql = qq~
	SELECT layout_id, name
	  FROM $TBMA_ARRAY_LAYOUT
	 WHERE name LIKE '$organism%'
	 ~;
  @rows = $sbeams->selectSeveralColumns($sql);


  # Create hash of array layouts 
  my %array_layouts;
  foreach my $row (@rows) {
	my ($layout_id, $array_name) = @{$row};
	$array_name =~ /.*\_(\d+)-(\d+)/;
	my $low_val = $1;
	my $hi_val = $2;
	$array_layouts{$low_val,$hi_val} = $layout_id;
  }


  ## Get printing_batch information
  $sql = qq~
	SELECT slide_list, printing_batch_id
	FROM $TBMA_PRINTING_BATCH 
	WHERE slide_type_id = $slide_type_id
	AND record_status != 'D'
	~;
  my %printing_batches = $sbeams->selectTwoColumnHash($sql);


  ## Get slide information
  $sql = qq~
	SELECT slide_number, slide_id
	  FROM $TBMA_SLIDE
	 WHERE record_status != 'D'
	 ~;
  my %slides = $sbeams->selectTwoColumnHash($sql);


  ## Verify that, in the form, the user hasn't selected the array twice
  my %unique_check;
  for (my $m=0;$m<$array_count;$m++) {
	my $array = $parameters{'array_'.$m};
	if ($unique_check{$array}) {
	  $successful = 0;
	  $error_messages .= "<FONT COLOR=\"red\">It appears as if you're trying to associate multiple records with array $array</FONT><BR>\n";
	}
  }
  undef %unique_check;


  ## Verify that all the prerequisite records are created.
  for (my $m=0;$m<$array_count;$m++) {

	my $file = $parameters{'quantfile_'.$m}; 
	my $array = $parameters{'array_'.$m};
	$array_info{$array,'quantitation_file'} = $file;

	## Verify that Array Locations are correct
	if (-e $file) {
	  print "<FONT COLOR=\"green\">File $file: Location VERIFIED</FONT><BR>\n";
	}else {
	  $error_messages.= "<FONT COLOR=\"red\">$file is not valid</FONT><BR>\n";
	  $successful = 0;
	}

	## Verify that record from 'array' table exists and isn't taken
	$sql = qq~
	  SELECT COUNT(*)
	    FROM $TBMA_ARRAY
	   WHERE array_name = '$array'
	   ~;
	@rows = $sbeams->selectOneColumn($sql);
	unless (scalar(@rows) == 1) {
	  $successful = 0;
	  $error_messages .= qq~
		<FONT COLOR=\"red\">Array \#$array already has a record in SBEAMS.  Contact Array Core.</FONT><BR>
		~;
	}

	### LEGACY CODE: I think we can get rid of this error check!
	## Verify that we have an appropriate array layout
	my $foundit = 0;
	foreach my $key (keys %array_layouts){
	  my @temp = split /\W/,$key;
	  my $low_val = $temp[0];
	  my $hi_val = $temp[1];
	  if ($low_val <= $array && $hi_val >= $array) {
		$array_info{$array,'array_layout_id'} = $array_layouts{$key};
		print "$array_layouts{$key} found for array $array<BR>\n";
		$foundit++;
	  }
	}
	if ($foundit != 1) {
	  $successful = 0;
	  $error_messages .= qq~
		<FONT COLOR=\"red\">Error in determining array layout for array \#$array. Contact Array Core</FONT><BR>
		~;
	}


	### LEGACY CODE: I think we can get rid of this error check!
	## Verify that we have an appropriate printing batch
	$foundit = 0;
	foreach my $key (keys %printing_batches) {
	  my @temp = split /-/, $key;
	  my $low_val = $temp[0];
	  my $hi_val = $temp[1];
	  if ($low_val <= $array && $hi_val >= $array) {
		$array_info{$array,'printing_batch_id'} = $printing_batches{$key};
		$foundit++;
	  }
	}
	if ($foundit != 1) {
	  $successful = 0;
	  $error_messages .= qq~
		<FONT COLOR=\"red\">Error in determining printing batch for array \#$array. Contact Array Core</FONT><BR>
		~;
	}

	## Verify that we have a slide_id for each quantitation file
	# hack to remove seroes from beginning of number
	my $zeroless_array = scalar($array);
	$zeroless_array++;
	$zeroless_array--;
	unless (defined($slides{$zeroless_array})) {
	  $successful = 0;
	  $error_messages .= qq~
		<FONT COLOR=\"red\">No corresponding slide record for array \#$array.  Contact Array Core</FONT><BR>
		~;
	}

  }

  ## If there are any errors, report them now or continue with adding records to SBEAMS
  unless ($successful == 1) {
	print $error_messages;
	print "<BR><B>Due to the listed errors, this transaction failed.  Please go back and make the corrections.</B>";
	print "<INPUT TYPE=\"button\" VALUE=\"<--Back\" OnClick=\"history.go(-1)\"><BR>\n";
	return;
  }

  #########################################################
  ## At this point, we should be clear to INSERT records ##
  #########################################################
  
  # Determine price of all the arrays (NOTE: NO LABELING/HYBRIDIZATION COSTS ARE INCLUDED)
  $sql =  "SELECT price FROM $TBMA_ARRAY_REQUEST_OPTION WHERE option_key = '$analysis_type' AND option_type LIKE 'scanning%' ";
  @rows = $sbeams->selectOneColumn($sql);
  my $scan_cost = $rows[0];
  
  $sql = " SELECT price FROM $TBMA_SLIDE_TYPE WHERE slide_type_id = '$slide_type_id' ";
  @rows = $sbeams->selectOneColumn($sql);
  my $array_cost = $rows[0];

  my $price = $scan_cost + ($array_count * $array_cost);

  ## Start the transaction
#  print "<BR>\n BEGIN TRANSACTION <BR>\n";
  $sbeams->executeSQL("BEGIN TRANSACTION");

  ## Insert Array Request Records
  my %rowdata;
  my $rowdata_ref;

  $rowdata{'contact_id'} = $contact_id;
  $rowdata{'project_id'} = $project;
  $rowdata{'cost_scheme_id'} = $cost_scheme_id;
  $rowdata{'slide_type_id'} = $slide_type_id;
  $rowdata{'n_slides'} = $array_count;
  $rowdata{'n_samples_per_slide'} = 2;
  $rowdata{'hybridization_request'} = $parameters{'prepType'};
  $rowdata{'scanning_request'}= $analysis_type;
  $rowdata{'request_status'} = "Finished";
  $rowdata{'price'} = $price;
 	
  $rowdata_ref= \%rowdata;
  my $array_request_id;
  $array_request_id =  $sbeams->updateOrInsertRow(table_name=>$TBMA_ARRAY_REQUEST,
												  rowdata_ref=>$rowdata_ref,
												  insert=>1,
												  return_PK=>1,
												  add_audit_parameters=>1
												  );
  undef %rowdata;

  ## INSERT array_request_slide record for each array
  for (my $m=0;$m<$array_count;$m++) {
	my $array = $parameters{'array_'.$m};

	## Format array_id so that it's a five digit number (e.g. '2886' --> '02886')
  # BUGFIX - this actually never ran until the array ids got > 9999, whereupon
  # it caused an infinite loop.  Will comment out, since it was a no-op
#	while ($array =~ /\d{5}/){
#	  $array = "0".$array;
#	}

	$rowdata{'array_request_id'} = $array_request_id;
	$rowdata{'slide_index'}= $m;
	$rowdata_ref = \%rowdata;

	my $array_request_slide_id;
	$array_request_slide_id = $sbeams->updateOrInsertRow(table_name=>$TBMA_ARRAY_REQUEST_SLIDE,
														 rowdata_ref=>$rowdata_ref,
														 insert=>1,
														 return_PK=>1,
														 add_audit_parameters=>1);
	$array_info{$array,'array_request_id'} = $array_request_id;
	$array_info{$array,'array_request_slide_id'} = $array_request_slide_id;
	undef %rowdata;

	## INSERT array_request_sample, labeling record, and hybridization
	my $sample0_name  = substr( $parameters{'sample0name_'.$m}, 0, 46)."..";
	my $sample1_name  = substr( $parameters{'sample1name_'.$m}, 0, 46)."..";

	for (my $sample_index=0;$sample_index<2;$sample_index++) {

	  ## INSERT array_request_sample record
	  $rowdata{'array_request_slide_id'} = $array_request_slide_id;
	  $rowdata{'sample_index'} = $sample_index;

	  my $full_name = $parameters{'sample'.$sample_index.'name_'.$m};
	  $rowdata{'full_name'} = $full_name;
	  $rowdata{'name'} = substr($full_name, 0, 46)."..";

	  $rowdata{'labeling_method_id'} = $parameters{'sample'.$sample_index.'labmeth_'.$m};
	  $rowdata_ref = \%rowdata;

	  my $array_request_sample_id;
	  $array_request_sample_id = $sbeams->updateOrInsertRow (table_name=>$TBMA_ARRAY_REQUEST_SAMPLE,
															 rowdata_ref=>$rowdata_ref,
															 insert=>1,
															 return_PK=>1,
															 add_audit_parameters=>1);
	  $array_info{$array,'array_request_sample_'.$sample_index.'_id'} = $array_request_sample_id;
	  undef %rowdata;

	  ## INSERT Labeling Record
	  $rowdata{'array_request_sample_id'} = $array_request_sample_id;
	  $rowdata{'protocol_id'} = $parameters{'labprot_'.$m};
	  $rowdata{'date_labeled'} = $parameters{'labdate_'.$m};
	  $rowdata{'dilution_factor'} = "-1";
	  $rowdata{'volume'} = "-1";
	  $rowdata{'absorbance_lambda'} = "-1";
	  $rowdata{'absorbance_260'} = "-1";
	  $rowdata{'dye_lot_number'} = $parameters{'sample'.$sample_index.'dye_'.$m};
	  $rowdata_ref = \%rowdata;
	  my $labeling_id;
	  $labeling_id = $sbeams->updateOrInsertRow (table_name=>$TBMA_LABELING,
												 rowdata_ref=>$rowdata_ref,
												 insert=>1,
												 add_audit_parameters=>1);
	  $array_info{$array,'labeling_id'} = $labeling_id;
	  undef %rowdata;
	}


	## INSERT Array Record
   	$rowdata{'project_id'} = $project;
	$rowdata{'layout_id'} = $array_info{$array,'array_layout_id'};
	$rowdata{'printing_batch_id'} = $array_info{$array,'printing_batch_id'};
	$rowdata{'slide_id'} = $slides{$array};
	$rowdata{'array_name'} = $array;
	$rowdata{'array_request_slide_id'} = $array_request_slide_id;
	$rowdata_ref = \%rowdata;

	my $array_id;
	$array_id = $sbeams->updateOrInsertRow(table_name=>$TBMA_ARRAY,
										   rowdata_ref=>$rowdata_ref,
										   insert=>1,
										   return_PK=>1,
										   add_audit_parameters=>1);

	## Format array_id so that it's a five digit number (e.g. '2886' --> '02886')
	while ($array_id =~ /\A\d{5}\Z/){
	  $array_id = "0".$array_id;
	}

	$array_info{$array,'array_id'} = $array_id;


	undef %rowdata;

	## INSERT Hybridization Record
	$rowdata{'name'} = $sample0_name.'_vs_'.$sample1_name;
	$rowdata{'array_id'} = $array_id;
	$rowdata{'protocol_id'} = $parameters{'hybprot_'.$m};
	$rowdata{'date_hybridized'} = $parameters{'hybdate_'.$m};
	$rowdata{'comment'} = 'Created by ArrayRecorder.cgi';
	$rowdata_ref = \%rowdata;
	my $hybridization_id;
	$hybridization_id = $sbeams->updateOrInsertRow (table_name=>$TBMA_HYBRIDIZATION,
													rowdata_ref=>$rowdata_ref,
													insert=>1,
													return_PK=>1,
													add_audit_parameters=>1);
	$array_info{$array,'hybridization_id'} = $hybridization_id;
	undef %rowdata;
	

	## INSERT array_scan record
	$rowdata{'array_id'} = $array_id;
	$rowdata{'protocol_id'} = $parameters{'scanprot_'.$m};
	$rowdata{'data_flag'} = $parameters{'scanflag_'.$m};
	$rowdata{'date_scanned'} = $parameters{'scandate_'.$m};
	$rowdata{'resolution'} = '10.00';
	$rowdata{'stage_location'} = $parameters{'scanfile_'.$m};
	$rowdata{'comment'} = 'Created by ArrayRecorder.cgi';
	$rowdata_ref = \%rowdata;
	my $array_scan_id;
	$array_scan_id = $sbeams->updateOrInsertRow (table_name=>$TBMA_ARRAY_SCAN,
												 rowdata_ref=>$rowdata_ref,
												 insert=>1,
												 return_PK=>1,
												 add_audit_parameters=>1);
	$array_info{$array,'array_scan_id'} = $array_scan_id;
	undef %rowdata;

	## INSERT array_quantitation_record
	$rowdata{'array_scan_id'} = $array_scan_id;
	$rowdata{'protocol_id'} = $parameters{'quantprot_'.$m};
	$rowdata{'stage_location'} = $parameters{'quantfile_'.$m};
	$rowdata{'data_flag'} = $parameters{'quantflag_'.$m};
	$rowdata{'date_quantitated'} = $parameters{'quantdate_'.$m};
	$rowdata{'comment'} = 'Created by ArrayRecorder.cgi';
	$rowdata_ref = \%rowdata;
	my $array_quantitation_id;
	$array_quantitation_id = $sbeams->updateOrInsertRow (table_name=>$TBMA_ARRAY_QUANTITATION,
														 rowdata_ref=>$rowdata_ref,
														 insert=>1,
														 return_PK=>1,
														 add_audit_parameters=>1);
	$array_info{$array,'array_quantitation_id'} = $array_quantitation_id;
	undef %rowdata;
  }
  
  ## End transaction
#  print "<BR>\n COMMIT TRANSACTION <BR>\n";
  $sbeams->executeSQL("COMMIT TRANSACTION");

  ## Print Successful Handling Screen
  print qq~
	<B>Array Records Inserted Successfully!</B><BR>
	To see the array request record:<BR>
	<A HREF =\"$SERVER_BASE_DIR$CGI_BASE_DIR/Microarray/SubmitArrayRequest.cgi?TABLE_NAME=MA_ARRAY_REQUEST&array_request_id=$array_request_id\">$SERVER_BASE_DIR$CGI_BASE_DIR/Microarray/SubmitArrayRequest.cgi?TABLE_NAME=MA_ARRAY_REQUEST&array_request_id=$array_request_id</A><BR>
	<BR>
	To visit this project\'s homepage:<BR>
	<A HREF=\"$SERVER_BASE_DIR$CGI_BASE_DIR/Microarray/ProjectHome.cgi?set_current_project_id=$project\">$SERVER_BASE_DIR$CGI_BASE_DIR/Microarray/ProjectHome.cgi?set_current_project_id=$project</A><BR>
	~;

  ## Fire off an email alerting the admins that a request has been added.
  alert_admins($array_request_id);
  alert_developers($array_request_id,\%array_info);
}


###############################################################################
# alert_admins
###############################################################################
sub alert_admins{
  my $PK = shift @_;
  my $mailprog = "/usr/lib/sendmail";
  my $recipient_name = "Microarray_admin Contact";
  my $recipient = "bmarzolf\@systemsbiology.org";
  my $cc_name = "SBEAMS";
  my $cc = "edeutsch\@systemsbiology.org";
  my $current_username = $sbeams->getCurrent_username();

  #### But if we're running as a dev version then just mail to administrator
  if ($DBVERSION =~ /Dev/) {
	$recipient_name = $cc_name;
	$recipient = $cc;
  }

  open (MAIL, "|$mailprog $recipient,$cc") || croak "Can't open $mailprog!\n";
  print MAIL "From: SBEAMS <edeutsch\@db.systemsbiology.net>\n";
  print MAIL "To: $recipient_name <$recipient>\n";
  print MAIL "Cc: $cc_name <$cc>\n";
  print MAIL "Reply-to: $current_username <${current_username}\@systemsbiology.org>\n";
  print MAIL "Subject: Microarray request submission\n\n";
  print MAIL "A microarray request was just entered into SBEAMS by ${current_username}.  This was sent by ArrayRecorder.cgi\n\n";
  print MAIL "To see the request view this link:\n\n";
  print MAIL "$SERVER_BASE_DIR$CGI_BASE_DIR/Microarray/SubmitArrayRequest.cgi?TABLE_NAME=MA_ARRAY_REQUEST&array_request_id=$PK\n\n";
  close (MAIL);
  
  print "<BR><BR>An email was just sent to the Microarray_admin Group informing them of your request.<BR>\n";
}

###############################################################################
# alert_developers
###############################################################################
sub alert_developers{
  my $PK = shift @_;
  my $parameters_ref = shift @_;
  my %parameters = %{$parameters_ref};
  my $mailprog = "/usr/lib/sendmail";
  my $recipient_name = "Microarray_admin Developer Contact";
  my $recipient = "bmarzolf\@systemsbiology.org";
  my $current_username = $sbeams->getCurrent_username();

  open (MAIL, "|$mailprog $recipient") || croak "Can't open $mailprog!\n";
  print MAIL "From: SBEAMS <edeutsch\@db.systemsbiology.net>\n";
  print MAIL "To: $recipient_name <$recipient>\n";
  print MAIL "Reply-to: $current_username <${current_username}\@systemsbiology.org>\n";
  print MAIL "Subject: Microarray request submission\n\n";
  print MAIL "A microarray request was just entered into SBEAMS by ${current_username}.  This was sent by ArrayRecorder.cgi\n\n";
  print MAIL "To see the request view this link:\n\n";
  print MAIL "$SERVER_BASE_DIR$CGI_BASE_DIR/Microarray/SubmitArrayRequest.cgi?TABLE_NAME=MA_ARRAY_REQUEST&array_request_id=$PK\n\n";
  print MAIL "Here is a listing of the data that was inserted:\n";
  print MAIL "KEY(array,data type) \t VALUE\n";
  foreach my $key (keys %parameters) {
	print MAIL "$key  -  $parameters{$key}\n";
  }
  close (MAIL);
  
  print "<BR><BR>An email was just sent to the Microarray_admin Group informing them of your request.<BR>\n";
}