#!/usr/local/bin/perl

###############################################################################
# $Id: AssessDIALibrary 5692 2008-07-08 17:17:27Z dcampbel $
#
# SBEAMS is Copyright (C) 2000-2016 Institute for Systems Biology
# This program is governed by the terms of the GNU General Public License (GPL)
# version 2 as published by the Free Software Foundation.  It is provided
# WITHOUT ANY WARRANTY.  See the full description of GPL terms in the
# LICENSE file distributed with this software.
###############################################################################


###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
use lib qw (../../lib/perl);
use Data::Dumper;
use File::Basename;
use File::Copy qw( move copy );
use LWP::UserAgent;
use HTTP::Request;
use JSON;
use CGI;

use SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
#use SBEAMS::Connection::SBPage;
use SBEAMS::Connection::DataTable;
use SBEAMS::Connection::TabMenu;


use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;


###############################################################################
# Global Variables
###############################################################################
my $sbeams = new SBEAMS::Connection;
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);
my $atlas = new SBEAMS::PeptideAtlas;
$atlas->setSBEAMS($sbeams);

my $max_size = 200000;
$CGI::POST_MAX = 1024 * $max_size;

my $json = new JSON;
  
# Read input parameters
my $params = process_params();
      $log->info( "params processed" );

my $username = $sbeams->Authenticate( allow_anonymous_access => 1) || exit;
$sbeams->setSessionAttribute( key => 'PA_resource', value => 'DIAAtlas' );

# Get a list of accessible project_ids
my @project_ids = $sbeams->getAccessibleProjects();
my $project_ids = join( ",", @project_ids ) || '0';

my $show_image = 0;
my $tabMenu;

my %basespace = ( basespace_params => '' );
my $page = '';

{ # Main 

    # Authenticate or exit


    ## get current settings
    my $project_id = $sbeams->getCurrent_project_id();

#    print $sbeams->get_http_header();
    $atlas->display_page_header( tracker_type => 'swath' );


    # Get the HTML to display the tabs
    $tabMenu = $atlas->getTabMenu(
      parameters_ref => $params,
      program_name => $0,
    );

    my $css = $sbeams->printStyleSheet( module_only => 1 );

    $page .=<<"    END";
     <br>
       $css
     <br>
     <br>
    END

    if ( 1 ) {
      my $title = qq~
      <div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:150%;font-weight:700"  id=heading>
		<font color =#ff5f00 >|</font> DIA Library Assessment</div>
	<br>
      ~;
    #  $page .= $title;
      $page .= $tabMenu;
      $page .= qq~
    <script>
    </script>

      ~;

      if ( $params->{ion_library} ) {
        $page .= get_status_box("Analyzing library, may take several minutes") unless $params->{action} eq 'trigger';
        print $page;
        $page = analyze_library();
        $page .= get_status_box("");
      } else {
        $page .= qq~
        <script type='text/javascript'> 
        function sizeme () {
          var ionlib = document.getElementById( 'ion_library' );
          var libsize = ionlib.files[0].size
          var maxsize = 1024 * $max_size;
          var maxsizefriendly = Math.round($max_size/1000)
          if ( libsize > maxsize ) {
            alert( "For files larger than " + maxsizefriendly + " MB we request that you run DIALib-QC locally" );
            ionlib.value="";
          }
        };
//                 //binds to onchange event of your input field
//                 $('#ion_library').bind('change', function() {
//                 //this.files[0].size gets the size of your file.
//                 alert(this.files[0].size);
//                 });     
    </script>
        ~;
        $page .= get_subset_form();
      }
    }
    $page .= "<BR>";

    # Print what we already have, speed up apparent page loading time.
		print $page;

		$atlas->display_page_footer();
    $sbeams->setSessionAttribute( key => 'PA_resource', value => '' );

} # end main

sub get_status_box {

  my $msg = shift || '';
  my $wait = "\<img\ src=\"$HTML_BASE_DIR/images/wait_sm.gif\"\>\</img\>";
  if ( $msg ) {
  return qq~ 
      <div id='status' class=info_box width: 400px >$wait $msg</div><br><br>
      <script type='text/javascript'> 
      function set_status ( new_status ) {
        var status = document.getElementById( 'status' );
        status.innerHTML = '$wait' + new_status;
        return false;
      }
      function update_status ( new_status ) {
        var status = document.getElementById( 'status' );
        var curr_status = status.innerHTML;
        status.innerHTML = curr_status + new_status;
      }
      function clear_status () {
        var status = document.getElementById( 'status' );
        status.remove();
//        status.innerHTML = "";
      }
      </script>
    ~;
  } else {
    return "<script>clear_status()</script>"
  }
}

sub get_help_links {


  my %title2text = ( 
                     'ion_library' => "Ion library to be analyzed (required) ",
                     'pep_file'    => "Mapping file of reference proteome, protein/peptide TSV, one peptide per line. ",
                     'swaths_file' => "File of SWATH bins, format is lower mz bound, upper bound mz, one per line TAB delimited",
                     'col_defs' => "Print out definitions for all tests",
                     'skip_decoys' => "Skip DECOY assess in compiling library statistics",
                     'alt_decoy' => "Alternate prefix to denote DECOY assays, default is DECOY",
                     'assess_massdiff' => "Compute difference between assay m/z and theoretical values, report on outliers",
      );

  my %title2link;
  for my $title ( keys( %title2text ) ) {
    my $text = $title2text{$title};
    $title2link{$title} = qq~<TD BGCOLOR=E0E0E0><span title='$text' class=popup><IMG SRC='$HTML_BASE_DIR/images/greyqmark.gif' BORDER=0 ONCLICK="popitup('$CGI_BASE_DIR/help_popup.cgi?title=$title;text=$text;email_link=no');"></SPAN></TD>~;
  }
  return \%title2link;
}

sub get_protein_list_selector {

  my $sql =<<"  END";
  SELECT title, protein_list_id
  FROM $TBAT_DOMAIN_PROTEIN_LIST DPL
  JOIN $TB_CONTACT C ON DPL.owner_contact_id = C.contact_id
  WHERE project_id IN ( $project_ids )
  ORDER BY title
  END

  my $sth = $sbeams->get_statement_handle( $sql );

  my $select;

  while( my @row = $sth->fetchrow_array() ) {
    my $selected = ( $row[1] == $params->{domain_protein_list_id} ) ? 'selected' : '';
    my $title = $row[0];
    $title =~ s/known to be associated with human/associated with/g;
    my $option = "<option value=$row[1] $selected>$title </option>\n";
    $select .= $option;
  }
  $select .= "</select>\n";
  my $blank = ( $select =~ /selected/ ) ? '' : '<option selected value="">&nbsp;</option>';

  $select = qq~
  <select name=domain_protein_list_id id=domain_protein_list_id>
  $blank
  $select
  ~;

  return $select;
}

sub get_table_help {
  my %args = @_;
  my $name = $args{table};
  return '' unless $name;
  $args{mode} ||= 'section';
  my @entries;
  my $hidetext;
  my $showtext;
  my $heading;
  my $description;

  if ( $name eq 'build' ) {  
    @entries = ( { key => 'Build Name', value => 'The simple name for this build, usually contains organism, prophet cutoff, and other information. ' },
                 { key => 'Build Description', value => 'More detailed information about build. ' },
                 { key => 'Reference Database', value => 'Database to which peptides were mapped, generally different than search database.  This mapping is done by running BLAST, and allows the peptides to be mapped the the organism\'s genomic sequence. ' },
                 { key => 'Build Date', value => 'Date upon which build was finished. ' },
                 { key => '# Samples', value => 'The number of individual samples which comprise this build.  Each sample contains one or more LCMS/MS runs, and generally corresponds to a single scientific experiment.' } ,
                 { key => 'Distinct Peptides', value => 'This shows the number of distinct peptide sequences that were seen in this build.  Observations of the peptide in different charge states or with different modifications are coalesced.' } ,
                 { key => 'Total Observations ', value => 'The total number of spectra that yeilded identifications above the build threshold.  Observations of the same base peptide sequences multiple times or in various charge states/modifications, whould each contribute to the total' }
        );
                 
    $showtext = 'show row descriptions';
    $hidetext = 'hide row descriptions';
    $heading = 'Build Overview';
    $description= 'These values pertain to the atlas build as a whole';


  } elsif ( $name eq 'batch' ) {
    @entries = ( { key => 'ID', value => 'Database ID for this sample (search batch) ' },
                 { key => 'Sample_Name', value => 'Simple name for this sample/experiment. ' },
                 { key => '#_Spectra_Searched', value => 'The total number of spectra searched in the sample. ' },
                 { key => "#_Spectra_ID'd", value => 'The number of spectra identifed with a probability greater than the atlas threshold ' },
                 { key => '#_Distinct', value => 'The number of distinct peptide sequences, seen more than once (multiobs), in this build that are seen in this sample. ' },
                 { key => '#_Unique', value => "The number of distinct, multiobs peptides that are seen only in this sample (unique contribution).  This discriminates against smaller samples, and is less useful in atlas' with a large number of samples. " },
                 { key => '#_Progressive', value => 'Order-dependent unique multiobs peptides contributed by a given sample.  The contribution for each sample is based on the samples that have gone before it, so later samples tend to have a lower progressive contribution. ' },
                 { key => '#_Cumulative', value => 'Order-dependent cumulative number of unique multiobs peptides contributed to build by this and previous samples. ' },
                 { key => '#_Proteins', value => 'The number of canonical (highly distinguishable, non-redundant) protein sequences identified from the peptides in this sample.' },
                 { key => '#_Cum_Prots', value => 'Order-dependent cumulative number of canonical proteins contributed to build by this and previous samples.<br>Counts non-human contaminants, so final tally may be greater than Canonical Proteins count in Build Overview. ' },
#                 { key => 'Sens', value => 'The sensitivity of the Peptide Prophet model at a probablility of 0.9, the percent of true positives that would be included at that threshold was used as a cutoff. ' },
                 { key => 'FDR_(%)', value => 'The error rate of peptides above the threshold Peptide Prophet model at a probablility of 0.9, the percent of false positives that would be included at the build threshold. ' },
                 { key => 'Sample_Date', value => ''},
        );
    $heading = 'Sample Overview'; 
    $description = 'These values pertain to individual samples within the atlas';

  } elsif ( $name eq 'mayu' ) {
   @entries = ( { key => 'nr_runs', value => 'Number of MS runs contributing to this build '},
  
		{ key => 'nr_files', value => 'Always 1 '},
  
		{ key => 'mFDR', value => 'Data in current row applies to all data meting this PSM (spectrum) FDR threshold. '},
		{ key => 'target_PSM', value => 'Number of non-decoy PSMs at this mFDR (counts peptides mappable to protein reference set only)'},
  
		{ key => 'decoy_PSM', value => 'Number of decoy PSMs at this mFDR '},
  
		{ key => 'FP_PSM', value => 'Number of false positive PSMs predicted by Mayu for this mFDR. Usually near, but not exactly the same as, the number of decoys. '},
  
		{ key => 'TP_PSM', value => 'target_PSM - FP_PSM '},
  
		{ key => 'target_pepID', value => 'Number of non-decoy unique peptides at this mFDR (counts peptides mappable to protein reference set only) '},
  
		{ key => 'decoy_pepID', value => 'Number of decoy unique peptides at this mFDR '},
  
		{ key => 'FP_pepID', value => 'Number of false positive unique peptides predicted by Mayu for this mFDR. Usually near, but not exactly the same as, the number of decoys. '},
  
		{ key => 'FP_pepID_stdev', value => ' '},
  
		{ key => 'TP_pepID', value => 'target_pepID - FP_pepID '},
  
		{ key => 'pepFDR', value => 'Peptide FDR (unique peptides)'},
  
		{ key => 'target_protID', value => 'Number of non-decoy protein identifications at this mFDR. Applied to the covering set of proteins -- a set that is close to the smallest necessary to explain all the pepIDs. Includes all canonicals and some possibly_distinguished. '},
  
		{ key => 'decoy_protID', value => 'Number of decoy protein identifications at this mFDR. '},
  
		{ key => 'FP_protID', value => 'Number of false postiive protein identifications predicted by Mayu for this mFDR.  Usually near, but not exactly the same as, the number of decoys. '},
  
		{ key => 'FP_protID_stdev', value => ' '},
  
		{ key => 'TP_protID', value => 'target_protID - FP_protID '},
  
		{ key => 'protFDR', value => 'Protein FDR. The largest value in this column is the protein FDR for the entire build. '},
		{ key => 'lFDR1, lFDR5, lFDR10,2 lFDR5', value => 'Local protein FDR, computed over the previous step (i.e. between the previous row in the table and the current row), the previous 5 steps, the previous 10 steps, and the previous 25 steps.<br>Often there are fewer than 25 rows in the table, in which case column lFDR25 is uninformative. '},
  
		{ key => 'target_protIDs, decoy_protIDs, etc.', value => 'Same as above, except for singleton proteins (those identified by only one PSM) only. '},
		{ key => 'target_protIDns, decoy_protIDns, etc.', value => 'Same as above, except for multiply-observed proteins only. '},
  
        );
    $heading = 'Mayu'; 
    $description = 'Reiter L, Claassen M, et al., Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry, Mol Cell Proteomics. 2009 Nov;8(11):2405-17 ';
  }


  return unless @entries;
  return \@entries if $args{mode} eq 'entries_only';

  my $help = $atlas->get_table_help_section( name => $name,
                                             description => $description,
                                             heading => $heading,
                                             entries => \@entries,
                                             showtext => $showtext,
                                             hidetext => $hidetext  );
  return $help;

} # end get_table_help


sub get_library_table {

  my $build_id = shift;

  my $help = qq~
   <br>
   <div style="font-family:Barlow, Arial, sans-serif;font-size:150%;font-weight:bold" id=heading> Library Download </div>
  </div>
  ~;
#   <div id=help style="width:800px"> Download SWATH/DIA libraries in any of the supported formats. 
#   <br><br>

  my $format_constraint = '';
  if ( $params->{format} ) {
    $format_constraint = "AND file_format = '$params->{format}'";
  }

  my $sql = qq~
  SELECT dia_library_id, dia_library_name, set_tag, instrument_type_name,
  organism_name, DIL.comment, md5sum, file_path, file_format, is_master,
  px_identifier, contributors, coverage_statement, 
  publication_url, publication_title, description
  FROM $TBAT_DIA_LIBRARY DIL 
  JOIN $TBAT_DIA_LIBRARY_SET DILS ON DILS.dia_library_set_id = DIL.dia_library_set_id
  JOIN $TBAT_INSTRUMENT_TYPE IT ON IT.instrument_type_id = DIL.instrument_type_id
  JOIN $TB_ORGANISM O ON O.organism_id = DIL.organism_id
  WHERE project_id IN ( $project_ids )
  AND DIL.record_status = 'N'
  $format_constraint
  ORDER BY DIL.dia_library_set_id, dia_library_name, instrument_type_name
  ~;
# 0 dia_library_id
# 1 dia_library_name
# 2 set_tag
# 3 instrument_type_name
# 4 organism_name
# 5 DIL.comment
# 6 md5sum
# 7 file_path
# 8 file_format
# 9 is_master
# 10 px_identifier
# 11 contributors
# 12 converage_statement
  my $sth = $sbeams->get_statement_handle( $sql );
  my %libraries; 
  my %tag2comment;
  my %display_format = ( peakview => 'Peakview',
                         openswath => 'OpenSWATH',
                         TraML => 'TraML',
                         sptxt => 'Speclib' );

  my @libs;
  while( my @row = $sth->fetchrow_array() ) {
    push @libs, $row[2] unless $libraries{$row[2]};
    $libraries{$row[2]} ||= [];
    $row[8] = $display_format{$row[8]} || $row[8]; 
    push @{$libraries{$row[2]}}, \@row;
    $tag2comment{$row[2]} = $row[5];
  }
  my $content = $help;

#  for my $lib ( sort { $b cmp $a} ( keys( %libraries ) ) ) {
  for my $lib ( @libs ) {
    my @lib_data = ( [ qw( Name Accession Instrument Format Size ), 'Get Libraries' ] );
    for my $lib_file ( @{$libraries{$lib}} ) {
      my $fname = basename( $lib_file->[7] ); 

      $sbeams->makeSBEAMSTempLink( path => $lib_file->[7],
                               linkname => $lib_file->[6],
                               relative => 0 );

      my $dwn = "<a href=$CGI_BASE_DIR/downloadFile.cgi?name=$fname;format=tsv;tmp_file=$lib_file->[6];raw_download=1>Download</a>";
      if ( $basespace{url_params} ) {
        $dwn = "<a href=GetDIALibs?mode=download_libs;action=download;name=$fname;tmp_file=$lib_file->[6];$basespace{url_params}>Download</a>";
      }
      my $size = -s $lib_file->[7];
#      if ( !$size ) {
#        die Dumper( $lib_file ) unless -e $lib_file->[7];
#      }
      $size = hr_size( $size, $lib_file->[7] );
      my $cust = '';
      if ( $lib_file->[8] =~ /peakview/i ||
           $lib_file->[8] =~ /openswath/i ||
           $lib_file->[8] =~ /mprophet/i ) { 
        if ( $lib_file->[9] eq 'Y' ) {
          my $basespace_url_params = ";$basespace{url_params}" || '';
          $cust = "<a href=GetDIALibs?mode=subset_libs;lib_id=$lib_file->[0]$basespace_url_params>Customize</a>" 
        }
      }
      my $accession = 'SAL' . sprintf( "%05i", $lib_file->[0] );
      $lib_file->[0] = $accession;
#      $lib_table->addRow( [ @{$lib_file}[1,5,3,8,6], $dwn . '&nbsp;&nbsp;' . $cust ] );
      push @lib_data, [ @{$lib_file}[1,0,3,8], $size, $dwn . '&nbsp;&nbsp;' . $cust ];
    }


    my ( $tr, $link ) = $sbeams->make_table_toggle( name => $lib_data[1]->[0],
                                                 visible => 0,
                                                 tooltip => 'Show/Hide Section',
                                                 showtext => 'Show library files',
                                                 hidetext => 'Hide library files',
                                                 imglink => 1,
                                                 textlink => 1,
                                                  sticky => 1 );




    my $lib_table = $atlas->encodeSectionTable( header => 1, 
                                                 width => '800',
                                               tr_info => $tr,
                                                align  => [ qw(left left left left left left center) ],
                                                  rows => \@lib_data,
                                           chg_bkg_idx => 3, 
                                              bg_color => '#EAEAEA',
                                              sortable => 0,
                                              table_id => $lib,
                                           close_table => 1,
                                            );

#    die Dumper( $lib_table );
#    die Dumper( $libraries{$lib} );

# 0 dia_library_id
# 1 dia_library_name
# 2 set_tag
# 3 instrument_type_name
# 4 organism_name
# 5 DIL.comment
# 6 md5sum
# 7 file_path
# 8 file_format
# 9 is_master
# 10 px_identifier
# 11 contributors
# 12 converage_statement
# 13 publication_url
# 14 publication_title
# 15 description

    # Hokey way to pull out some set-specific items.
    my $lib_zero = $libraries{$lib}->[0];

    # Publication info
    my $publication = '';
    if ( $lib_zero->[13] && $lib_zero->[14] ) {
      if ( $lib_zero->[13] =~ /In press/ || $lib_zero->[13] =~ /Submitted/ ) {
        $publication = "Publication: <i>$lib_zero->[14]</i> ($lib_zero->[13]) <br>";
      } else {
        $publication = "Publication: <i>$lib_zero->[14]</i> (<a href='$lib_zero->[13]'>View</a>) <br>";
      }
    }
    my $description = '';
    if ( $lib_zero->[15] ) {
      $description = "$lib_zero->[15]<br>";
    }

    my $px_link = '';
    if ( $lib_zero->[10] ) {
      if ( $lib_zero->[10] =~ /^PXD/ ) {
        $px_link = "(<a href='http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$lib_zero->[10]' target=_px title='View dataset $lib_zero->[10] at Proteome Exchange'>$lib_zero->[10]</a>)";
      } else {
        $px_link = "(<a href='https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?identifier=$lib_zero->[10]' target=_px title='View dataset $lib_zero->[10] at Proteome Exchange'>$lib_zero->[10]</a>)";
      }



    }

    $lib_zero->[12] .= '<br>' if $lib_zero->[12];
    $content .= qq~
    <br>
     <span style="font-family:Helvetica, Arial, sans-serif;font-size:110%;font-weight:bold" id=heading> $lib </span><br>
     $description
     $lib_zero->[11] $px_link <br>
     $lib_zero->[12] 
     $publication
     $link <table>$lib_table
    <br>
    ~;
  }
  return $content;

}

sub hr_size {
  my $size = shift;
  if ( !$size ) {
    my $file = shift;
    $log->info( "why does $file have no size?" );
  }
  my @sfx = ( '', 'KB', 'MB', 'GB', 'TB', 'PB' );

#  $log->info( "in sizer, original size is $size" );
  my $i = 0;
  while ( $size > 1024 ) {
    $size = $size / 1024;
    $i++;
  }
  my $format_size = sprintf( "%.1f", $size ) . " $sfx[$i]";
#  $log->info( "in sizer, formatted size is $format_size" );
  return $format_size;
}

sub get_btxt {
  my @tags = @_;
  my $max = 0;
  for my $tag ( @tags ) {
    $max = length( $tag ) if length( $tag ) > $max;
  }
  my %btxt;
  for my $tag ( @tags ) {
    my $len = length( $tag );
    my $delta = $max - $len;
    my $pad = 0;
    if ( $delta ) {
      $pad = int($delta/2 + 0.5);
    }
    my $prepad = '&nbsp;' x $pad; 
    my $postpad = '&nbsp;' x ($max - $len - $pad); 
    $btxt{$tag} = $prepad . $tag . $postpad;
  }
  return \%btxt; 

}


sub analyze_library {

  $log->info( "in analyze library");
  die unless $params->{ion_library};
  $log->info( "params->ion_library exists");

  my $mode = $params->{mode};
  my $mod_type = $params->{mod_type};
  $log->info( "Mode is $mode\n");
  $log->info( "Mod type is $mod_type\n");
  
  #my $filebase = $sbeams->getRandomString( num_chars => 20 );
  my $filebase = "Charu";
  my $run_dir = $PHYSICAL_BASE_DIR . '/tmp/PeptideAtlas/AssessDIALibrary/';
  $log->info( $run_dir );

  my $exec = "/regis/sbeams/bin/ionlibrary/assess_swathlib.pl ";
  my $sfile = $filebase . '.swaths';
  if ( $params->{swaths_file} ) {
    open SWATHS, ">$run_dir/$sfile";
    my $name = $q->param('swaths_file');
    while ( my $line = <$name> ) {
      print SWATHS $line;
    }
    close SWATHS;
    $exec .= "--swath $run_dir/$sfile ";
  }

  my $pfile = $filebase . '.ppeps';
  if ( $params->{pep_file} ) {
    open PEPS, ">$run_dir/$pfile";
    my $name = $q->param('pep_file');
    while ( my $line = <$name> ) {
      print PEPS $line;
    }
    close PEPS;
  } else {
    open PEPS, ">$run_dir/$pfile" || die;
    close PEPS;
  }
  $exec .= " --pep $run_dir/$pfile ";
  if ( -e "$run_dir/$pfile" ) {
    $log->info( "created peps file $run_dir/$pfile" );
  } else {
    print "Error: Failed to create peps file!\n";
    $log->info( "failed to create peps" );
    return '';
  }
  if ( $params->{massdiff} ) {
    $exec .= ' --assess ';
  }
  
  my $libfile = $filebase . '.ionlib';
  open IONLIB, ">$run_dir/$libfile";
  $log->info("created libfile");
  my $name = $q->param('ion_library');
  while ( my $line = <$name> ) {
    print IONLIB $line;
  }
  close IONLIB;
  $log->info("populated libfile");
  $exec .= " --ion $run_dir/$libfile --output $run_dir/$filebase  ";

  if ( $mod_type ) {
    if ( $mod_type eq 'filter' ) {
      $exec .= " --filter ";
    } else {
      $exec .= " --correct ";
    }
  } else {
    $exec .= " --full_stats --rt_stats --coldef --invert ";
  }

  if ( !-e "$run_dir/$libfile" ) {
    print "Error: Failed to create file!\n";
    return '';
  }
  $log->info( $exec );
  my $lib = $params->{ion_library};
  
#  print "Going to execute $exec\n";

  my $result = `$exec 2>&1`;
  $log->info( $result );
  if ( -e "$run_dir/$filebase.QC.tsv" ) {
    
    my $update_libname = `perl -pi -e 's/$libfile/$lib/gm' "$run_dir/$filebase.QC.tsv"`;
    $log->info( "QC file found, updated libname from $libfile to $lib: $update_libname\n" );
  } else {
    $log->info( "QC file not found, stopping\n");
    return;
  }
  open QC, "$run_dir/$filebase.QC.tsv";
  my $return = '';
  my $format;
  my @data = ( [ qw( Attribute Value Definition ) ] );
  while ( my $line = <QC> ) {
    chomp $line;
    my @line = split( /\t/, $line );
    if ( $line[0] eq 'library' ) {
      $line[1] = $lib;
    } elsif ( $line[0] eq 'format' ) {
      $format = $line[1];
    }
    $return .= "<tr><td><b>$line[0]</b></td><td align=right>$line[1]</td><td>$line[2]</td></tr>\n";
    push @data, \@line;
  }
  close QC;
  $return .= "</table>\n";
  exec `rm -f $run_dir/$libfile $run_dir/$pfile $run_dir/$sfile`;

  if ( $mod_type ) {
    `rm -f $run_dir/$filebase.QC.tsv`;
  } else { # no plots in filter mode
    print_js_status("Finished analysis, plotting results...", 1);
    my $exec = "/regis/sbeams/bin/ionlibrary/DIALib-QC_RPlot.pl $run_dir/$filebase.fullstats $run_dir/$filebase.RT ";
    $log->info( $exec );
    my $pdf_out = `$exec 2>&1`;
    $log->info( $pdf_out );
  }

   my ( $html, $rs_name ) = $atlas->encodeSectionTable( header => 1, 
                                                        width => '600',
#                                                      tr_info => $args{tr},
                                                       align  => [ qw(left right left) ],
                                                  rs_headings => [ qw( Attribute Value Definition ) ],
                                                         rows => \@data,
                                                 rows_to_show => 200,
                                                      colspan => 3,
                                                     max_rows => 2500,
                                               manual_widgets => 1,
#                                                    help_text => $help_text,
                                                  chg_bkg_idx => 0, 
#                                                 set_download => 'Download analysis', 
#                                                download_form => $download_select, 
                                                    rs_params => { set_name => 'changeme' },
                                                  file_prefix => 'DIA_Lib_Analysis', 
#                                                     bg_color => '#EAEAEA',
                                                     sortable => 1,
                                                     table_id => 'pabst',
                                                  close_table => 1,
                                                     );



  my $downloads = qq~
  <table style="border-collapse: collapse" border=0 width=500>
  <tr>
    <td colspan=2 align=left><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:150%;font-weight:700" id=heading><font color =#ff5f00 >|</font><b> Download Files</b></div></td>
  </tr>
  <tr></tr>
  <tr class="cellblock_top"> 
    <td>&nbsp;</td> 
    <td>&nbsp;</td> 
  </tr>
  ~;

  my %type2download = ( pdf => 'Graphical depiction of library characteristics (PDF) and Library summary statistics (TSV)',
                        tsv =>  'Library summary statistics, also depicted in table below (TSV)',
                        mz_corrected => "Input library with m/z values re-computed ($format)",
                        clean => "Input library with problem assays filtered out ($format)",
                        problem => "Problem assays filtered from input library ($format)" );

  my $lib_base = $lib;
  $lib_base =~ s/\.[^\.]+$//;
  if ( -e "$PHYSICAL_BASE_DIR/tmp/PeptideAtlas/AssessDIALibrary/$filebase.pdf" ) {

    
    my $ln_out = `cp $PHYSICAL_BASE_DIR/tmp/PeptideAtlas/AssessDIALibrary/$filebase.pdf $PHYSICAL_BASE_DIR/tmp/PeptideAtlas/AssessDIALibrary/$lib_base.pdf`;
    $log->info( $ln_out );
    
    $downloads .= qq~
      <tr class=cellblock>
        <td align=left> <a href=$HTML_BASE_DIR/tmp/PeptideAtlas/AssessDIALibrary/$lib_base.pdf> $lib_base.pdf </a> &nbsp;&nbsp;</td>
        <td align=left><i>&nbsp; $type2download{pdf}</i></td>
      </tr>
    ~;
  }
  for my $type ( qw( QC.tsv mz_corrected clean problem ) ) {
    my $fname = $lib_base . '.' . $type;
    my $path_dir = "$PHYSICAL_BASE_DIR/tmp/PeptideAtlas/AssessDIALibrary/";
    my $rel_path_dir = '/tmp/PeptideAtlas/AssessDIALibrary/';
    my $path =  $path_dir . '/' . $filebase . '.' . $type;
    my $rel_path =  $rel_path_dir . '/' . $filebase . '.' . $type;

    if ( !-e $path ) {
      $path = $run_dir . '/' . $filebase . '.ionlib.' . $type;
      next unless -e $path;
      $rel_path =  $rel_path_dir . '/' . $filebase . '.ionlib.' . $type;
    }
    $sbeams->makeSBEAMSTempLink( path => $path,
                             linkname => $fname,
                             relative => 0 );

    my $dwn = "<a href=$CGI_BASE_DIR/downloadFile.cgi?name=$fname;format=tsv;tmp_file=$rel_path;raw_download=1>$fname</a>";
                        
    my $link = qq~  
    <tr class=cellblock>
      <td align=left>$dwn &nbsp;&nbsp;</td>
      <td align=left><i>&nbsp; $type2download{$type}</i></td>
    </tr>
    ~;
    $downloads .= $link;
  }

  $downloads .= qq~
  <tr class=cellblock_bottom>
    <td colspan=2>&nbsp;</td>
  </tr>
  </table>
  ~;
  $html = '' if $mod_type;

  return "$downloads  <br><br><table>$html</table>";
}
  
sub get_subset_form {
  
  my $help = qq~
  <br>
   <div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:150%;font-weight:700" id=heading>
	  <font color =#ff5f00 >|</font> DIA Library Assessment</div>
   <div id=help style="width:720px; font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700"><br><br> This form allows you to assess various properties of a DIA library in OpenSWATH, Spectronaut, or Peakview formats.
  </div>
  ~;
  
  my $title2help = get_help_links();

  my $form = qq~
  $help
  <script type=text/javascript>
  function check_form(mode) {
    if ( mode == "submit" ) {
      var ionlib = document.getElementById( 'ion_library' );
      if ( ionlib.value.length == 0 ) {
        alert( "You must provide an ion library to use this feature" );
        return false;
      }
      return true;
    } else if ( mode == "assess" ) {
      var correct_cell = document.getElementById( 'correct_cell' );
      correct_cell.className = 'inactive_text';
      var filter_cell = document.getElementById( 'filter_cell' );
      filter_cell.className = 'inactive_text';
      var csubmit_cell = document.getElementById( 'correct_submit' );
      csubmit_cell.className = 'inactive_text';
      var correct = document.getElementById( 'correct' );
      correct.checked = false;
      var filter = document.getElementById( 'filter' );
      filter.checked = false;
      var asubmit = document.getElementById( 'assess_submit' );
      asubmit.className = 'active_text';
    } else if ( mode == "correct" ) {
      var correct_cell = document.getElementById( 'correct_cell' );
      correct_cell.className = 'active_text';
      var filter_cell = document.getElementById( 'filter_cell' );
      filter_cell.className = 'active_text';
      var csubmit = document.getElementById( 'correct_submit' );
      csubmit.className = 'active_text';
      var asubmit = document.getElementById( 'assess_submit' );
      asubmit.className = 'inactive_text';
    } else if ( mode == "blur" ) {
      if ( document.getElementById( "analyze" ).checked ) {
        var correct = document.getElementById( 'correct' );
        correct.checked = false;
        var filter = document.getElementById( 'filter' );
        filter.checked = false;
      }
    } else if ( mode == "correct_submit" ) {
      if ( document.getElementById( "analyze" ).checked ) {
        return false;
      }
      var correct = document.getElementById( 'correct' );
      var filter = document.getElementById( 'filter' );
      if ( correct.checked == false && filter.checked == false ) {
        alert( "Must select either filter or mz_correct" );
        return false;
      }
    } else if ( mode == "assess_submit" ) {
      if ( document.getElementById( "update" ).checked ) {
        return false;
      }
    } else {
      alert( mode );
    }
  }
  function popitup(url) {
    newwindow=window.open( url ,'helpwin','height=400,width=300,dependent=yes,screenX=5000,screenY=50,scrollbars=yes,resizable=yes');
    if (window.focus) {newwindow.focus()}
    return false;
  }

  </script>
  <br><br>

  <table style="border-collapse: collapse" border=0 width=500>
  <form method=post id=assess onSubmit="return check_form('submit')" enctype="multipart/form-data">
  <br>
  <div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:150%;font-weight:700" id=heading>Input data</div>
  <tr class="cellblock_top">
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
  </tr>
  <tr class=cellblock>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Ion Library:</div></i></b></td>
    $title2help->{ion_library}
    <td><input type=file name=ion_library id=ion_library onchange="sizeme()"></input></td>
  </tr>
  <tr class=cellblock>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> SWATHs definition file (optional):</div></i></b></td>
    $title2help->{swaths_file}
    <td><input type=file name=swaths_file id=swaths_file></input></td>
  </tr>
  <tr class=cellblock>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Proteome mapping file (optional):</div></i></b></td>
    $title2help->{pep_file}
    <td><input type=file name=pep_file id=pep_file></input></td>
  </tr>
  <tr class="cellblock_bottom">
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
  </tr>
  <tr><td/></tr>
  <tr><td/></tr>
  <tr><td/></tr>
  <tr><td/></tr>
  <tr><td colspan=3 align=left><b><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:150%;font-weight:700" id=heading><input type=radio id=analyze value=analyze name=mode checked onclick=check_form('assess')>Analyze Library</b></div></td></tr>
  <tr class="cellblock_top">
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
  </tr>
  <tr class=cellblock>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Assess mass diffs(optional):</div></i></b></td>
    $title2help->{assess_massdiff}
    <td>Yes<input type=radio name=massdiff checked=yes>&nbsp;No<input type=radio name=massdiff></td>
  </tr>
  <tr class=cellblock>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Print definitions for each test(optional):</div></i></b></td>
    $title2help->{col_defs}
    <td>Yes<input type=radio name=coldefs checked=yes>&nbsp;No<input type=radio name=coldefs></td>
  </tr>
  <tr class=cellblock>
    <td>&nbsp;</td>
    <td colspan=2 align=left><input type=submit value='Assess Ion Library' id=assess_submit class=active_text onclick="return check_form('assess_submit')"></input></td>
  </tr>
  <tr class="cellblock_bottom">
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
  </tr>
  <tr><td/></tr>
  <tr><td/></tr>
  <tr><td/></tr>
  <tr><td/></tr>

  <tr><td colspan=3 align=left><b><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:150%;font-weight:700" id=heading><input type=radio id=update value=correct name=mode onclick=check_form('correct') >Correct Library</b></div></td></tr>
  <tr class="cellblock_top">
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
  </tr>
  <tr class=cellblock>
    <td align=right class=inactive_text id=filter_cell><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Filter problem assays:</div></i></b></td>
    $title2help->{assess_massdiff}
    <td><input type=radio name=mod_type id=filter value=filter onclick=check_form('blur') >&nbsp;</td>
  </tr>
  <tr class=cellblock>
    <td align=right class="inactive_text" id=correct_cell><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Re-compute m/z values:</div></i></b></td>
    $title2help->{assess_massdiff}
    <td><input type=radio name=mod_type id=correct value=correct onclick=check_form('blur')>&nbsp;</td>
  </tr>
  <tr class=cellblock>
    <td>&nbsp;</td>
    <td colspan=2 align=left><input id=correct_submit type=submit value='Repair Ion Library' class=inactive_text onclick="return check_form('correct_submit')"></input></td>
  </tr>
  <tr class="cellblock_bottom">
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
  </tr>
  </table>
  
  </form>
  <br>
  <br>
  ~;



  return $form;
  my $extra = qq~

  <tr class=cellblock>
    <td align=right><b><i>Skip DECOYs(optional):</i></b></td>
    $title2help->{skip_decoys}
    <td>Yes<input type=radio name=skip_decoy checked=no>&nbsp;No<input checked=yes type=radio name=skip_decoy></td>
  </tr>
  <tr class=cellblock>
    <td align=right><b><i>Alternate DECOY string (optional):</i></b></td>
    $title2help->{alt_decoy}
    <td>Yes<input type=text length=25></td>
  </tr>

  ~;


}

sub process_params {
  my $params = {};
#  for my $p ( qw( skip_decoy swaths_file massdiff ion_library coldefs ) ) {
#    $params->{$p} = $q->param( $p );
#  }
#  $log->info( $params );
$q = new CGI;
  $sbeams->parse_input_parameters( q => $q, parameters_ref => $params );
  $sbeams->processStandardParameters( parameters_ref => $params );
  return( $params );
}


sub js_redirect {
  my $url = shift || return;
  print qq~<script type=text/javascript> window.location.replace( "$url" ); </script>~;
}

sub print_js_status {
  my $msg = shift or return;
  $log->info( $msg );
  my $replace = shift || 0;

  if ( $replace ) {
    print "<script type=text/javascript> set_status( '$msg' ); </script>" ;
  } else {
    print "<script type=text/javascript> update_status( '<br>$msg' ); </script>" ;
  }
}


sub get_build_path {
  my %args = @_;
  return unless $args{build_id};
  my $path = $atlas->getAtlasBuildDirectory( atlas_build_id => $args{build_id} );
  $path =~ s/DATA_FILES//;
  return $path;
}

sub get_draw_chart_function {
	my $sample_arrayref = shift || return '';

	my @samples;
	for my $s ( @{$sample_arrayref} ) {
		push @samples, [ $s->[1], $s->[4], $s->[7] ];
	}
	my $GV = SBEAMS::Connection::GoogleVisualization->new();
  my ( $chart ) = $GV->setDrawBarChart(  samples => \@samples,
                                    	data_types => [ 'string', 'number', 'number' ],
                                      	headings => [ 'Sample', 'Distinct peptides (n_obs > 1)', 'Cumulative peptides (n_obs > 1)' ],
                                      show_table => 0,
                                 truncate_labels => 24
 	);
	my $header = $GV->getHeaderInfo();
  return ( $chart, $header );
}


sub get_public_libsets {

  my $sql = qq~
  SELECT set_tag, instrument_type_name,
  organism_name, px_identifier, contributors, coverage_statement,
  COUNT(*) AS cnt
  FROM $TBAT_DIA_LIBRARY DIL 
  JOIN $TBAT_DIA_LIBRARY_SET DILS ON DILS.dia_library_set_id = DIL.dia_library_set_id
  JOIN $TBAT_INSTRUMENT_TYPE IT ON IT.instrument_type_id = DIL.instrument_type_id
  JOIN $TB_ORGANISM O ON O.organism_id = DIL.organism_id
  WHERE project_id IN ( $project_ids )
  AND DIL.record_status = 'N'
  GROUP BY set_tag, instrument_type_name,
  organism_name, px_identifier, contributors, coverage_statement
  ORDER BY set_tag, instrument_type_name
  ~;
# 0 set_tag
# 1 instrument_type_name
# 2 organism_name
# 3 px_identifier
# 4 contributors
# 5 coverage_statement
# 6 cnt

  my $sth = $sbeams->get_statement_handle( $sql );
  my %sets;
  while ( my @row = $sth->fetchrow_array() ) {
    if ( $sets{$row[0]} ) {
      $sets{$row[0]}->{inst} = $row[1] if $row[1] =~ /TripleTOF/;
      $sets{$row[0]}->{lib_cnt} += $row[6];
    } else {
      my $px = ( $row[3] ) ? 
               ( $row[3] =~ /^PXD/ ) ? "<a href='http://groteomecentral.proteomexchange.org/cgi/GetDataset?ID=$row[3]' target=_px>$row[3]</a>" :
                                       "<a href='https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?identifier=$row[3]' target=_px>$row[3]</a>" :
               $sbeams->makeInactiveText( 'na' );
        
        $sbeams->makeInactiveText( 'na' );
      $row[5] =~ s/Proteome Coverage//gi;
      $sets{$row[0]} = { inst => $row[1],
                         lib_cnt => $row[6],
                         px => $px,
                         org => $row[2],
                         cov => $row[5],
                         cont => $row[4] };
    }
  }
  use JSON;
  my $json = new JSON;
  my $jstr = $json->encode( \%sets );

#  my @lib_data = ( [ qw( Library Organism Instrument Contributors Coverage ProteomeExchange NumFiles ) ] );
#  my @lib_data = ( [ qw( Library Instrument Contributors Coverage ) ] );
  my @lib_data = ( [ 'Library', 'Proteome Coverage', 'Contributors' ] );
  for my $lib ( sort( keys( %sets ) ) ) {
#    push @lib_data, [ $lib, $sets{$lib}->{org}, $sets{$lib}->{inst}, $sets{$lib}->{cont}, $sets{$lib}->{cov}, $sets{$lib}->{px}, $sets{$lib}->{lib_cnt} ];
#    push @lib_data, [ $lib, $sets{$lib}->{inst}, $sets{$lib}->{cont}, $sets{$lib}->{cov} ];
    push @lib_data, [ $lib, $sets{$lib}->{cov}, $sets{$lib}->{cont} ];
  }

  my $lib_table = $atlas->encodeSectionTable( header => 1, 
                                               width => '800',
                                              align  => [ qw(left left left left ) ],
                                                rows => \@lib_data,
                                         chg_bkg_idx => 0, 
                                            bg_color => '#EAEAEA',
                                            sortable => 0,
                                              nowrap => [1,2,3],
                                            table_id => 'libraries',
                                          table_only => 1,
                                         close_table => 1,
                                            );

  print qq~
    <html>
    <head></head>
    <body>
    $lib_table
    </body>
    </html>
  ~;
  


}

__DATA__