#!/usr/local/bin/perl 


###############################################################################
# Set up all needed modules and objects
###############################################################################
use strict;
use Getopt::Long;
use FindBin;

use lib qw (../../lib/perl);
use vars qw ($sbeams $sbeamsMOD $q $current_contact_id $current_username
             $PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $DATABASE
             $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
             @MENU_OPTIONS);
use DBI;
use CGI::Carp qw(fatalsToBrowser croak);
use POSIX;

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

use SBEAMS::Inkjet;
use SBEAMS::Inkjet::Settings;
use SBEAMS::Inkjet::Tables;

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::Inkjet;
$sbeamsMOD->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);

#use CGI;
#$q = new CGI;


###############################################################################
# Set program name and usage banner for command like use
###############################################################################
$PROG_NAME = $FindBin::Script;
$USAGE = <<EOU;
Usage: $PROG_NAME [OPTIONS] key=value kay=value ...
Options:
  --verbose n         Set verbosity level.  default is 0
  --quiet             Set flag to print nothing at all except errors
  --debug n           Set debug flag

 e.g.:  $PROG_NAME [OPTIONS] [keyword=value],...

EOU

#### Process options
unless (GetOptions(\%OPTIONS,"verbose:s","quiet","debug:s")) {
  print "$USAGE";
  exit;
}

$VERBOSE = $OPTIONS{"verbose"} || 0;
$QUIET   = $OPTIONS{"quiet"} || 0;
$DEBUG   = $OPTIONS{"debug"} || 0;
if ($DEBUG) {
  print "Options settings:\n";
  print "  VERBOSE = $VERBOSE\n";
  print "  QUIET = $QUIET\n";
  print "  DEBUG = $DEBUG\n";
}


###############################################################################
# Set Global Variables and execute main()
###############################################################################
$PROGRAM_FILE_NAME = 'ProjectHome.cgi';
main();
exit(0);



###############################################################################
# Main Program:
#
# Call $sbeams->Authenticate() and exit if it fails or continue if it works.
###############################################################################
sub main {

  #### Do the SBEAMS authentication and exit if a username is not returned
  exit unless ($current_username = $sbeams->Authenticate(
    #connect_read_only=>1,
    #allow_anonymous_access=>1,
    #permitted_work_groups_ref=>['Proteomics_user','Proteomics_admin'],
  ));


  #### 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);


  #### Decide what action to take based on information so far
  if ($parameters{action} eq "???") {
  } else {
    $sbeamsMOD->printPageHeader();
    print_javascript();
    handle_request(ref_parameters=>\%parameters);
    $sbeamsMOD->printPageFooter();
  }

} # end main


###############################################################################
# print_javascript 
##############################################################################
sub print_javascript {

    my $uri = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/";

print qq~
<SCRIPT LANGUAGE="Javascript">
<!--
<!-- $uri -->
function viewRequest(status){
    var site;
    if (status == 'old') {
	var id = document.requests.chooser.options[document.requests.chooser.selectedIndex].value;
	site = "${uri}SubmitArrayRequest.cgi?TABLE_NAME=IJ_array_request&array_request_id="+id;
    }
    else {
	site = "${uri}SubmitArrayRequest.cgi?TABLE_NAME=IJ_array_request&ShowEntryForm=1";
    }
    var newWindow = window.open(site);
}

function viewImage(status){
    var site;
    if (status == 'old') {
	//alert ("scan images not available to be viewed.  Will be developed later");
    var id = document.images.chooser.options[document.images.chooser.selectedIndex].value
    var site = "${uri}ManageTable.cgi?TABLE_NAME=IJ_array_scan&array_scan_id="+id
    }
    else {
	//alert ("scan images not on a network share.");
        var site = "${uri}ManageTable.cgi?TABLE_NAME=$TBIJ_ARRAY_SCAN&ShowEntryForm=1";
    }
    var newWindow = window.open(site);
}

function viewQuantitation(status){
    var site;
    if (status == 'old') {
	var id = document.quantitations.chooser.options[document.quantitations.chooser.selectedIndex].value;
	site = "${uri}ManageTable.cgi?TABLE_NAME=IJ_array_quantitation&array_quantitation_id="+id;
    }
    else {
	site = "${uri}ManageTable.cgi?TABLE_NAME=IJ_array_quantitation&ShowEntryForm=1";
    }
    var newWindow = window.open(site);
}

function actionLogFile(action){
    var id = document.outputFiles.logChooser.options[document.outputFiles.logChooser.selectedIndex].value;
    if (action == "get") {
	getFile(id);
    } else {
	viewFile(id);
    }
}		
    
function actionRepFile(){
  var id = document.outputFiles.repChooser.options[document.outputFiles.repChooser.selectedIndex].value;
  getFile(id);
}
function actionMergeFile(){
  var id = document.outputFiles.mergeChooser.options[document.outputFiles.mergeChooser.selectedIndex].value;
  getFile(id);
}
function actionSigFile(){
  var id = document.outputFiles.sigChooser.options[document.outputFiles.sigChooser.selectedIndex].value;
  getFile(id);
}
function actionCloneFile(){
  var id = document.outputFiles.cloneChooser.options[document.outputFiles.cloneChooser.selectedIndex].value;
  getFile(id);
}


function getFile(id){
    var site = "$uri/ViewFile.cgi?action=download&FILE_NAME="+id;
    window.location = site;
}
		
function viewFile(id){
    var site = "$uri/ViewFile.cgi?action=view&FILE_NAME="+id;
    var newWindow = window.open(site);
}

function startMev(project_id){
    document.tavForm.project_id.value=project_id;
    
    var tavList = document.tavForm.tavChooser;
    var tavArray;
    var isFirst = 1;
    for (var i=0;i<tavList.length;i++){
	if (tavList.options[i].selected) {
	    if (isFirst == 1){
		isFirst = 0;
		tavArray = tavList.options[i].value;
	    }else {
		tavArray += "," + tavList.options[i].value;
	    }
	}
    }
    
    document.tavForm.selectedFiles.value = tavArray;
    document.tavForm.submit();
    
}
    
    
    //Determines what browser is being used and what OS is being used.
    // convert all characters to lowercase to simplify testing
    var agt=navigator.userAgent.toLowerCase();
    
// *** BROWSER VERSION ***
    var is_nav  = ((agt.indexOf('mozilla')!=-1) && (agt.indexOf('spoofer')==-1)
                && (agt.indexOf('compatible') == -1) && (agt.indexOf('opera')==-1)
									 && (agt.indexOf('webtv')==-1));
var is_ie   = (agt.indexOf("msie") != -1);
var is_opera = (agt.indexOf("opera") != -1);

// *** PLATFORM ***
    var is_win   = ( (agt.indexOf("win")!=-1) || (agt.indexOf("16bit")!=-1) );
var is_mac    = (agt.indexOf("mac")!=-1);
var is_sun   = (agt.indexOf("sunos")!=-1);
var is_linux = (agt.indexOf("inux")!=-1);
var is_unix  = ((agt.indexOf("x11")!=-1) || is_linux);

//-->
</SCRIPT>
~;
return 1;
}

###############################################################################
# Handle Request
###############################################################################
sub handle_request {
  my %args = @_;


  #### Process the arguments list
  my $ref_parameters = $args{'ref_parameters'}
    || die "ref_parameters not passed";
  my %parameters = %{$ref_parameters};


  #### Define some generic varibles
  my ($i,$element,$key,$value,$line,$result,$sql);
  my @rows;


  #### Define variables for Summary Section
  my $project_id = $parameters{PROJECT_ID} || $sbeams->getCurrent_project_id; 
  my $pi_first_name = '';
  my $pi_last_name = '';
  my $username = '';
  my $project_name = 'NONE';
  my $project_tag = 'NONE';
  my $project_status = 'N/A';
  my $pi_contact_id;
  my (%array_requests, %array_scans, %quantitation_files);

  #### Show current user context information
  $sbeams->printUserContext();
  $current_contact_id = $sbeams->getCurrent_contact_id();

  #### Get information about the current project from the database
  $sql = qq~
	SELECT P.name,P.project_tag,P.project_status, C.first_name, C.last_name, C.contact_id, UL.username
	  FROM $TB_PROJECT P
	  JOIN $TB_CONTACT C ON ( P.PI_contact_id = C.contact_id )
	  JOIN $TB_USER_LOGIN UL ON ( UL.contact_id = C.contact_id)
	WHERE P.project_id = '$project_id'
  ~;
  @rows = $sbeams->selectSeveralColumns($sql);

  if (@rows) {
    ($project_name,$project_tag,$project_status,$pi_first_name,$pi_last_name,$pi_contact_id,$username) = @{$rows[0]};
  }

  #### print_tabs
#  my @tab_titles = ("Summary","Management","Data Analysis", "Permissions");
  my @tab_titles = ("Summary","MIAME Status","Management","Data Analysis","Permissions");
  my $tab_titles_ref = \@tab_titles;
  my $page_link = 'ProjectHome.cgi';

  #### Summary Section 
  if ($parameters{'tab'} eq "summary"){
      $sbeamsMOD->print_tabs(tab_titles_ref=>$tab_titles_ref,
			     page_link=>$page_link,
			     selected_tab=>0);
      print_summary_tab(parameters_ref=>\%parameters); 
  }
  elsif($parameters{'tab'} eq "miame_status") { 
      $sbeamsMOD->print_tabs(tab_titles_ref=>$tab_titles_ref,
			     page_link=>$page_link,
			     selected_tab=>1);
      print_miame_status_tab(); 
  }
  elsif($parameters{'tab'} eq "management") { 
      $sbeamsMOD->print_tabs(tab_titles_ref=>$tab_titles_ref,
			     page_link=>$page_link,
			     selected_tab=>2);
      print_management_tab();
  }
  elsif($parameters{'tab'} eq "data_analysis") {
      $sbeamsMOD->print_tabs(tab_titles_ref=>$tab_titles_ref,
			     page_link=>$page_link,
			     selected_tab=>3);
      print_data_analysis_tab()
  }
  elsif($parameters{'tab'} eq "permissions") {
      $sbeamsMOD->print_tabs(tab_titles_ref=>$tab_titles_ref,
			     page_link=>$page_link,
			     selected_tab=>4);
      print_permissions_tab(ref_parameters=>$ref_parameters); 
  }
  else{
      $sbeamsMOD->print_tabs(tab_titles_ref=>$tab_titles_ref,
			     page_link=>$page_link,
			     selected_tab=>0);
      print_summary_tab(parameters_ref=>\%parameters);
  }
  return;

}# end handle_request



###############################################################################
# print_summary_tab
###############################################################################
sub print_summary_tab {
  my %args = @_;
  my $SUB_NAME = "print_summary_tab";
  
	my $parameters_ref = $args{'parameters_ref'} || die "ERROR[$SUB_NAME] No parameters passed\n";
	my %parameters = %{$parameters_ref};
  my $apply_action=$parameters{'action'} || $parameters{'apply_action'} || 'QUERY';

	## HACK: If set_current_project_id is a parameter, we do a 'QUERY' instead of a 'VIEWRESULTSET'
	if ($parameters{set_current_project_id}) {$apply_action = 'QUERY';}

  ## Define standard variables
  my ($sql, @rows);
  my $current_contact_id = $sbeams->getCurrent_contact_id();
  my (%array_requests, %array_scans, %quantitation_files);
  my $project_id = $sbeams->getCurrent_project_id();
  my ($project_name, $project_tag, $project_status, $project_desc);
  my ($pi_first_name, $pi_last_name, $pi_contact_id, $username);

  #### Get information about the current project from the database
  $sql = qq~
	SELECT P.name,P.project_tag,P.project_status,P.description,C.first_name,C.last_name,C.contact_id,UL.username
	  FROM $TB_PROJECT P
	  JOIN $TB_CONTACT C ON ( P.PI_contact_id = C.contact_id )
	  JOIN $TB_USER_LOGIN UL ON ( UL.contact_id = C.contact_id)
	WHERE P.project_id = '$project_id'
  ~;
  @rows = $sbeams->selectSeveralColumns($sql);

  if (@rows) {
    ($project_name,$project_tag,$project_status,$project_desc,$pi_first_name,$pi_last_name,$pi_contact_id,$username) = @{$rows[0]};
  }

  #### Print out some information about this project
  print qq~

<H1>Summary of $project_name (ID \#$project_id):</H1>
<B>
<A HREF="$CGI_BASE_DIR/$SBEAMS_SUBDIR/ManageTable.cgi?TABLE_NAME=project&project_id=$project_id">[Edit Project Description]</A>
</B><BR>

<TABLE WIDTH="100%" BORDER=0>
<TR><TD><IMG SRC="$HTML_BASE_DIR/images/space.gif" WIDTH="20" HEIGHT="1"></TD>
    <TD COLSPAN="2" WIDTH="100%"><B>PI: </B>$pi_first_name $pi_last_name</TD></TR>
<TR><TD></TD><TD COLSPAN="2" WIDTH="100%"><B>Status:</B> $project_status</TD></TR>
<TR><TD></TD><TD COLSPAN="2"><B>Project Tag:</B> $project_tag</TD></TR>
<TR><TD></TD><TD COLSPAN="2"><B>Description:</B>$project_desc</TD></TR>
  ~;

  #### Get all the array information for this project
  my $n_array_requests = 0;
  my $n_array_scans = 0;
  my $n_array_quantitations = 0;
  if ($project_id > 0) {

      $sql = qq~
	  SELECT array_request_id, n_slides, date_created 
	  FROM $TBIJ_ARRAY_REQUEST
	  WHERE project_id = '$project_id'
	  AND record_status != 'D'
      ~;
      @rows = $sbeams->selectSeveralColumns($sql);
      foreach my $row(@rows){
	  my @temp_row = @{$row};
	  $array_requests{$temp_row[0]} = "$temp_row[2] ($temp_row[1] slides)";
	  $n_array_requests++;
      }


      $sql = qq~
	  SELECT COUNT (ASCAN.array_scan_id) AS 'Scans', 
	         COUNT (AQ.array_quantitation_id) AS 'Quantitations'
            FROM $TBIJ_ARRAY A
            LEFT JOIN $TBIJ_ARRAY_SCAN ASCAN ON (A.array_id = ASCAN.array_id)
	    LEFT JOIN $TBIJ_ARRAY_QUANTITATION AQ ON ( AQ.array_scan_id = ASCAN.array_scan_id )
           WHERE A.project_id = '$project_id'
             AND A.record_status != 'D'
	     ~;
      @rows = $sbeams->selectSeveralColumns($sql);
     ($n_array_scans, $n_array_quantitations) = @{$rows[0]};
  }

  print qq~
<TR><TD></TD><TD COLSPAN="2"><B>Array Requests: $n_array_requests</B></TD></TR>
<TR><TD></TD><TD COLSPAN="2"><B>Array Scans: $n_array_scans</B></TD></TR>
<TR><TD></TD><TD COLSPAN="2"><B>Array Quantitations: $n_array_quantitations</B></TD></TR>
<TR><TD></TD><TD COLSPAN="2"><B>Access Privileges:</B><A HREF="$CGI_BASE_DIR/ManageProjectPrivileges">[View/Edit]</A></TD></TR>    
<TR><TD></TD><TD><IMG SRC="$HTML_BASE_DIR/images/space.gif" WIDTH="20" HEIGHT="1"></TD></TR>
</TABLE>
$LINESEPARATOR
  ~;

####  Project Status Section ####
	$sql = qq~
SELECT	A.array_id,A.array_name,
	ARSM1.name AS "Sample1Name",ARSM2.name AS "Sample2Name",
	AR.array_request_id,ARSL.array_request_slide_id,
	AR.date_created AS "date_requested",
	PB.printing_batch_id,PB.date_started AS "date_printed",
	H.hybridization_id,H.date_hybridized,
	ASCAN.array_scan_id,ASCAN.date_scanned,ASCAN.data_flag AS "scan_flag",
	AQ.array_quantitation_id,AQ.date_quantitated,AQ.data_flag AS "quan_flag",
	ARSM1.array_request_sample_id AS "array_request_sample_id1",
	ARSM2.array_request_sample_id AS "array_request_sample_id2"
  FROM $TBIJ_ARRAY_REQUEST AR
  LEFT JOIN $TBIJ_ARRAY_REQUEST_SLIDE ARSL ON ( AR.array_request_id = ARSL.array_request_id )  
  LEFT JOIN $TBIJ_ARRAY_REQUEST_SAMPLE ARSM1 ON ( ARSL.array_request_slide_id = ARSM1.array_request_slide_id AND ARSM1.sample_index=0)
  LEFT JOIN $TBIJ_ARRAY_REQUEST_SAMPLE ARSM2 ON ( ARSL.array_request_slide_id = ARSM2.array_request_slide_id AND ARSM2.sample_index=1)
  LEFT JOIN $TBIJ_ARRAY A ON ( A.array_request_slide_id = ARSL.array_request_slide_id )
  LEFT JOIN $TBIJ_PRINTING_BATCH PB ON ( A.printing_batch_id = PB.printing_batch_id )
  LEFT JOIN $TBIJ_HYBRIDIZATION H ON ( A.array_id = H.array_id )
  LEFT JOIN $TBIJ_ARRAY_SCAN ASCAN ON ( A.array_id = ASCAN.array_id )
  LEFT JOIN $TBIJ_ARRAY_QUANTITATION AQ ON ( ASCAN.array_scan_id = AQ.array_scan_id )
 WHERE AR.project_id=$project_id
   AND ARSL.array_request_slide_id IS NOT NULL
   AND ( AR.record_status != 'D' OR AR.record_status IS NULL )
   AND ( A.record_status != 'D' OR A.record_status IS NULL )
   AND ( PB.record_status != 'D' OR PB.record_status IS NULL )
   AND ( H.record_status != 'D' OR H.record_status IS NULL )
   AND ( ASCAN.record_status != 'D' OR ASCAN.record_status IS NULL )
   AND ( AQ.record_status != 'D' OR AQ.record_status IS NULL )
 ORDER BY A.array_name,AR.array_request_id,ARSL.array_request_slide_id
        ~;

  my $manage_table_url = "$CGI_BASE_DIR/Inkjet/ManageTable.cgi?TABLE_NAME=IJ_";
  my %url_cols = ('array_name' => "${manage_table_url}array&array_id=%0V",
		  'Sample1Name' => "${manage_table_url}array_request_sample&array_request_sample_id=%17V",
		  'Sample2Name' => "${manage_table_url}array_request_sample&array_request_sample_id=%18V",
		  'date_requested' => "$CGI_BASE_DIR/Inkjet/SubmitArrayRequest.cgi?TABLE_NAME=IJ_array_request&array_request_id=%4V",
		  'date_printed' => "${manage_table_url}printing_batch&printing_batch_id=%7V", 
		  'date_hybridized' => "${manage_table_url}hybridization&hybridization_id=%9V", 
		  'date_scanned' => "${manage_table_url}array_scan&array_scan_id=%11V", 
		  'date_quantitated' => "${manage_table_url}array_quantitation&array_quantitation_id=%14V", 
		  );

  my %hidden_cols = ('array_id' => 1,
		     'array_request_id' => 1,
		     'printing_batch_id' => 1,
		     'hybridization_id' => 1,
		     'array_scan_id' => 1,
		     'array_quantitation_id' => 1,
		     'array_request_sample_id1' => 1,
		     'array_request_sample_id2' => 1,
		     );

#########################################################################
	my %resultset = ();
	my $resultset_ref = \%resultset;
	my %max_widths;
  my %rs_params = $sbeams->parseResultSetParams(q=>$q);
	my $base_url = "$CGI_BASE_DIR/Inkjet/ProjectHome.cgi";

  #### If the apply action was to recall a previous resultset, do it
  if ($apply_action eq "VIEWRESULTSET") {
    $sbeams->readResultSet(
      resultset_file=>$rs_params{set_name},
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>\%parameters,
      resultset_params_ref=>\%rs_params,
    );
  }

  #### Build ROWCOUNT constraint
  $parameters{row_limit} = 5000
    unless ($parameters{row_limit} > 0 && $parameters{row_limit}<=1000000);
  my $limit_clause = $sbeams->buildLimitClause(row_limit=>$parameters{row_limit});


	#### If the action contained QUERY, then fetch the results from
	#### the database
	if ($apply_action =~ /QUERY/i) {

    #### Fetch the results from the database server
    $sbeams->fetchResultSet(sql_query=>$sql,
														resultset_ref=>$resultset_ref,
														);

		#### Store the resultset and parameters to disk resultset cache
		$rs_params{set_name} = "SETME";
		$sbeams->writeResultSet(resultset_file_ref=>\$rs_params{set_name},
														resultset_ref=>$resultset_ref,
														query_parameters_ref=>\%parameters,
														resultset_params_ref=>\%rs_params,
														query_name=>"$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME",
														);
  }

	#### Set the column_titles to just the column_names
	my @column_titles = @{$resultset_ref->{column_list_ref}};

	#### Display the resultset
	$sbeams->displayResultSet(resultset_ref=>$resultset_ref,
														query_parameters_ref=>\%parameters,
														rs_params_ref=>\%rs_params,
														url_cols_ref=>\%url_cols,
														hidden_cols_ref=>\%hidden_cols,
														max_widths=>\%max_widths,
														column_titles_ref=>\@column_titles,
														base_url=>$base_url,
														);

	#### Display the resultset controls
	$sbeams->displayResultSetControls(resultset_ref=>$resultset_ref,
																		query_parameters_ref=>\%parameters,
																		rs_params_ref=>\%rs_params,
																		base_url=>$base_url,
																		);
}


###############################################################################
# print_miame_status_tab
###############################################################################
sub print_miame_status_tab {
  my %args = @_;
  my $SUB_NAME = "print_miame_status_tab";
  
  ## Decode argument list
  my $project_id = $sbeams->getCurrent_project_id();

  ## Define standard variables

  print qq!

<H1>MIAME Status:</H1>
<IMG SRC="$HTML_BASE_DIR/images/space.gif" WIDTH="100%" HEIGHT="1"><BR>
<TABLE CELLSPACING="5">
<TR><TD></TD></TR>
<TR>
  <TD>Experiment Design</TD>
  <TD><A HREF="MIAMEStatus.cgi?tab=experiment_design">Detailed Information</A></TD>
</TR>
<TR>
  <TD>Array Design</TD>
  <TD><A HREF="MIAMEStatus.cgi?tab=array_design">Detailed Information</A></TD>
</TR>
<TR>
  <TD>Sample Information</TD>
  <TD><A HREF="MIAMEStatus.cgi?tab=sample_information">Detailed Information</A></TD>
</TR>
<TR>
  <TD>Labeling and Hybridization</TD>
  <TD><A HREF="MIAMEStatus.cgi?tab=labeling_and_hybridization">Detailed Information</A></TD>
</TR>
<TR>
  <TD>Measurements</TD>
  <TD><A HREF="MIAMEStatus.cgi?tab=measurements">Detailed Information</A></TD>
</TR>
<TR>
  <TD></TD>
  <TD><IMG SRC="$HTML_BASE_DIR/images/space.gif" WIDTH="20" HEIGHT="1"></TD>
</TR>
</TABLE><BR>
<B>Links</B><BR>
<A HREF="http://www.mged.org/Workgroups/MIAME/miame.html" target="_blank">-MIAME Website</A><BR>
<A HREF="../../doc/Inkjet/MIAME_checklist.doc">-Download MIAME Checklist</A>
$LINESEPARATOR
      !;
  return;
}
  

###############################################################################
# print_management_tab
###############################################################################
sub print_management_tab {
  my %args = @_;
  my $SUB_NAME = "print_management_tab";
  
  ## Decode argument list
  my $project_id = $sbeams->getCurrent_project_id();

  ## Define standard variables
  my ($sql, @rows);
  my (%array_requests, $n_array_requests);
  my (%array_scans, $n_array_scans);
  my (%quantitation_files, $n_quantitation_files);

  $sql = qq~
      SELECT array_request_id, n_slides, date_created 
      FROM $TBIJ_ARRAY_REQUEST
      WHERE project_id = '$project_id'
      AND record_status != 'D'
      ~;
  @rows = $sbeams->selectSeveralColumns($sql);
  foreach my $row(@rows){
      my @temp_row = @{$row};
      $array_requests{$temp_row[0]} = "$temp_row[2] ($temp_row[1] slides)";
      $n_array_requests++;
  }
  
  $sql = qq~
      SELECT ASCAN.array_scan_id, ASCAN.stage_location
      FROM $TBIJ_ARRAY_SCAN ASCAN
      JOIN $TBIJ_ARRAY A ON ( A.array_id = ASCAN.array_id )
      JOIN $TBIJ_ARRAY_QUANTITATION AQ ON ( AQ.array_scan_id = ASCAN.array_scan_id )
      WHERE A.project_id = '$project_id'
      AND ASCAN.record_status != 'D'
      AND A.record_status != 'D'
      AND AQ.record_status != 'D'
      ~;
  %array_scans = $sbeams->selectTwoColumnHash($sql);
  
  $sql = qq~
      SELECT AQ.array_quantitation_id, AQ.stage_location
      FROM $TBIJ_ARRAY_SCAN ASCAN
      JOIN $TBIJ_ARRAY A ON ( A.array_id = ASCAN.array_id )
      JOIN $TBIJ_ARRAY_QUANTITATION AQ ON ( AQ.array_scan_id = ASCAN.array_scan_id )
      WHERE A.project_id = '$project_id'
      AND ASCAN.record_status != 'D'
      AND A.record_status != 'D'
      AND AQ.record_status != 'D'
      ~;
  %quantitation_files = $sbeams->selectTwoColumnHash($sql);
  
  foreach my $key (keys %array_scans) {
      $n_array_scans++;
  }
  foreach my $key (keys %quantitation_files){
      $n_quantitation_files++;
  }

  print qq~
<H1>Project Management:</H1>
<IMG SRC="$HTML_BASE_DIR/images/space.gif" WIDTH="100%" HEIGHT="1">
  ~;

  print qq~
<FORM NAME="requests">
<TABLE>
<TR><TD><B>Array Requests</B></TD></TR>
<TR><TD><SELECT NAME="chooser">
  ~;
  
  foreach my $key(keys %array_requests) {
      print qq~ <OPTION value = "$key">$array_requests{$key} ~;
  }

  print qq~
</SELECT></TD></TR>
<TR>
  <TD>
  <INPUT TYPE="button" name="arButton" value="Go To Record" onClick="viewRequest('old')">
  <INPUT TYPE="button" name="newARButton" value="Add New Record" onClick="viewRequest('new')">
  </TD>
</TR>
</TABLE>
</FORM>
	
<BR>
      
<FORM NAME="images">
<TABLE>
<TR><TD><B>Array Images</B></TD></TR>
<TR><TD><SELECT name="chooser">
        ~;
  
  foreach my $key(keys %array_scans) {
      my $name = $array_scans{$key};
      $name =~ s(^.*/)();
      print qq~ <OPTION value="$key">$name ~;
  }
  
  print qq~
</SELECT></TD></TR>
<TR>
  <TD>
  <INPUT TYPE="button"name="aiButton" value="Go To Record" onClick="viewImage('old')">
  <INPUT TYPE="button"name="newAIButton" value="Add New Record" onClick="viewImage('new')">
  </TD>
</TR>
</TABLE>
</FORM>
      
<BR>

<FORM NAME="quantitations">
<TABLE>
<TR><TD><B>Array Quantitation</B></TD></TR>
<TR><TD><SELECT name="chooser">
        ~;

  foreach my $key (keys %quantitation_files) {
      my $name = $quantitation_files{$key};
      $name =~ s(^.*/)();
      print qq~ <OPTION value="$key">$name ~;
  }
  print qq~
</SELECT></TD></TR>
<TR>
  <TD>
  <INPUT TYPE="button"name="aqButton"value="Go to Record" onClick="viewQuantitation('old')">
  <INPUT TYPE="button"name="newAQButton"value="Add New Record" onClick="viewQuantitation('new')">
  </TD>
</TR>
</TABLE>
</FORM>
$LINESEPARATOR
  ~;
  return;
}

  

###############################################################################
# print_data_analysis_tab
###############################################################################
sub print_data_analysis_tab {
  my %args = @_;
  my $SUB_NAME = "print_data_analysis_tab";
  
  ## Decode argument list
  my $project_id = $sbeams->getCurrent_project_id();

  ## Define standard variables
  my ($sql, @rows);

  # Data Analysis Section
  my $output_dir = "/net/arrays/Pipeline/output/project_id/".$project_id;
  my @pdf_list = glob("$output_dir/*.pdf");
  my @log_list = glob("$output_dir/*.log");
  my @sig_list = glob("$output_dir/*.sig");
  my @clone_list = glob("$output_dir/*.clone");
  my @merge_list = glob("$output_dir/*.merge");
  my @rep_list = glob("$output_dir/*.rep");
  my @matrix_list = glob("$output_dir/matrix_output");
  my @zip_file = glob ("$output_dir/*.zip");
  my @tav_list = glob ("$output_dir/*.tav");

  print qq~
<H1>Data Analysis:</H1>
<UL>
  <LI><A HREF="ProcessProject.cgi">Submit a New Job to the Pipeline</A>
  <LI><A HREF="http://db.systemsbiology.net/software/ArrayProcess/" TARGET="_blank">What is the Data Processing Pipeline?</A>
</UL>
$LINESEPARATOR
      ~;

	## Display TAV Options if there are such files
	if ($tav_list[0]) {
	print qq~
<FORM NAME="tavForm" METHOD="GET" ACTION="http://db.systemsbiology.net:8080/microarray/sbeams">
<INPUT TYPE="hidden" NAME="project_id" VALUE="">
<INPUT TYPE="hidden" NAME="selectedFiles" VALUE="">
<INPUT TYPE="hidden" NAME="tab" VALUE="data_analysis">
<TABLE>
<TR VALIGN="center"><TD><B>MeV Files</B></TD></TR>
<TR>
  <TD>
  <SELECT NAME="tavChooser" MULTIPLE SIZE="10">
        ~;
	foreach my $tav(@tav_list) {
	  my $temp = $tav;
	  $temp=~s(^.*/)();
	  print qq~<OPTION value="$temp">$temp~;
        }
	print qq~
  </SELECT>
  </TD>
  <TD>
  <A HREF="http://www.tigr.org/software/tm4/mev.html" TARGET="_blank"><IMG SRC="../../images/ma_mev_logo.gif"></A>
  </TD>
</TR>
<TR>
  <TD>
  <INPUT TYPE="button" name="mevButton" value="View Selected Files in MeV" onClick="Javascript:startMev($project_id)">
  </TD>
</TR>
<TR><TD></TD></TR>
</TABLE>
</FORM>
~;
      }

      print qq~
<FORM NAME="outputFiles" METHOD="POST">
<TABLE>
      ~;

  ## Display ZIP file Options if there are such files
  if ($zip_file[0]){
      $zip_file[0]=~ s(^.*/)();
      print qq~
<TR>
  <TD>
  <A HREF="ViewFile.cgi?action=download&FILE_NAME=$zip_file[0]"><B>Download zipped file of entire project directory</B></A>
  </TD>
</TR>
 <TR><TD></TD></TR>
 ~;
  }

  ## Display Rep File Options if there are such files
  if ($rep_list[0]){
    print qq~
<TR VALIGN="center"><TD><B>Rep Files</B></TD></TR>
<TR>
  <TD>
  <SELECT NAME="repChooser">
~;
    foreach my $rep(@rep_list) {
      my $temp = $rep;
      $temp =~ s(^.*/)();
      print qq~<OPTION value="$temp">$temp~;
    }
    print qq~
  </SELECT>
  </TD>
</TR>
<TR>
  <TD><INPUT TYPE="button" name="repButton" value="download" onClick="Javascript:actionRepFile()"></TD>
</TR>
<TR><TD></TD></TR>
~;
  }

  ## Display Merge File  Options if there are such files
  if ($merge_list[0]) {
    print qq~
<TR>
  <TD><B>Merge Files</B></TD>
</TR>
<TR>
  <TD>
  <SELECT NAME="mergeChooser">
			 ~;
    foreach my $merge(@merge_list) {
	my $temp = $merge;
	$temp =~ s(^.*/)();
	print qq~<OPTION value="$temp">$temp~;
    }
    print qq~
  </SELECT>
  </TD>
</TR>
<TR>
  <TD><INPUT TYPE="button" name="repButton" value="download" onClick="Javascript:actionMergeFile()"></TD>
</TR>
<TR><TD></TD></TR>
  ~;
  }
	
  ## Display Clone File Options if there are such files
  if ($clone_list[0]) {
    print qq~
<TR>
  <TD><B>Clone Files</B></TD>
</TR>
<TR>
  <TD>
  <SELECT NAME="cloneChooser">
    ~;
    foreach my $clone(@clone_list) {
      my $temp = $clone;
      $temp =~ s(^.*/)();
      print qq~ <OPTION value="$temp">$temp~;
    }
    print qq~
  </SELECT>
  </TD>
</TR>
<TR>
  <TD>
  <INPUT TYPE="button" name="repButton" value="download" onClick="Javascript:actionCloneFile()">
  </TD>
</TR>
<TR><TD></TD></TR>
  ~;
  }

  ## Display Sig File Options if there are such files
  if ($sig_list[0]) {
    print qq~
<TR>
  <TD><B>Sig Files</B></TD>
</TR>
<TR>
  <TD>
  <SELECT NAME="sigChooser">
    ~;
    foreach my $sig(@sig_list) {
      my $temp = $sig;
      $temp =~ s(^.*/)();
      print qq~ <OPTION value="$temp">$temp~;
    }
    print qq~
  </SELECT>
  </TD>
</TR>
<TR>
  <TD><INPUT TYPE="button" name="repButton" value="download" onClick="Javascript:actionSigFile()"></TD>
</TR>
<TR><TD></TD></TR>
  ~;
  }

  ## Display Log Fil Options if there are such files
  if ($log_list[0]) {
    print qq~
<TR><TD><B>Log Files</B></TD></TR>
<TR>
  <TD>
  <SELECT NAME="logChooser">
  ~;

    foreach my $log(@log_list) {
      my $temp = $log;
      $temp =~ s(^.*/)();
      print qq~ <OPTION value="$temp">$temp~;
    }
    print qq~
  </SELECT>
  </TD>
</TR>
<TR>
  <TD>
  <INPUT TYPE="button" name="logButtonView" value="view" onClick="Javascript:actionLogFile('view')">
  <INPUT TYPE="button" name="logButtonGet" value="download" onClick="Javascript:actionLogFile('get')">
  </TD>
</TR>
  ~;
  }

  ## Finish up table
  print qq~
</TABLE>
</FORM>
$LINESEPARATOR
~;

  return;
}


###############################################################################
# print_permissions_tab
###############################################################################
sub print_permissions_tab {
  my %args = @_;
  #### Process the arguments list
  my $ref_parameters = $args{'ref_parameters'}
    || die "ref_parameters not passed";
  
  $sbeams->print_permissions_table(ref_parameters=>$ref_parameters, no_permissions=>1);
}