#!/usr/local/bin/perl

###############################################################################
# $Id$
#
# SBEAMS is Copyright (C) 2000-2021 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 SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
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 $json = new JSON;
  
# Read input parameters
my $params = process_params();

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 => '' );

{ # Main 

    # Authenticate or exit


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


    if ( $params->{mode} eq 'get_public_libsets' ) {
      $params->{output_format} ||= 'html';
      unless ( $params->{output_format} eq 'json' ) {
	print $sbeams->get_http_header();
      }
      get_public_libsets();
      exit;
    }

    $params->{action} ||= 'trigger';
    if ( $params->{appsessionuri} && $params->{authorization_code} ) {
      $basespace{basespace_params} = qq~
      <input type=hidden name=appsessionuri value=$params->{appsessionuri}></input>
      <input type=hidden name=authorization_code value='$params->{authorization_code}' />
      <input type=hidden name=upload_to_basespace value=yes />
      ~;
      $basespace{appsessionuri} = $params->{appsessionuri};
      $basespace{authorization_code} = $params->{authorization_code};
      $basespace{url_params} = ";authorization_code=$params->{authorization_code};appsessionuri=$params->{appsessionuri}";


      authenticate_to_basespace();
      get_appsession_properties();
#      $log->info( "mode is $params->{mode}" );
      $params->{mode} ||= $basespace{mode};
      $params->{format} ||= 'peakview';
#      $log->info( "mode is $params->{mode}" );
    }
    $params->{mode} ||= 'download_libs';

    my $program_name = ( $params->{mode} =~ /download/ ) ? 'DIA_library_download' : 'DIA_library_subset';
    my $page = $sbeams->getGifSpacer( 700 ) . "<BR>\n";

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

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

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

#    my $load_script = "set_toggle_box( 'protein_list_table' );sortables_init()";
    if ( $params->{lib_id} ) {
      $params->{mode} = 'subset_libs';
    }
    $params->{mode} ||= 'download_libs';
#    die "header coming";
    $atlas->display_page_header( tracker_type => 'swath' );

    if ( $params->{mode} eq 'subset_libs' ) {
      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> Custom Library Download </div>
      <br>
      ~;
     # $page .= $title;
      $page .= $tabMenu;
      $page .= get_status_box("Generating library, may take several minutes") unless $params->{action} eq 'trigger';
      print $page;
      $page = get_subset_form();

    } elsif ( $params->{mode} eq 'download_libs' ) {
      $page .= $tabMenu;
      if ( $params->{action} eq 'download' ) {
        $page .= get_status_box( "" );
        print $page;
        upload_to_basespace();

        $page = '';
      }
      $page .= get_library_table();
    }
    $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>";

  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 = 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;
      }
      </script>
    ~;
}

sub get_help_links {


  my %title2text = ( 'Library' => "Source library file to customize. <br><br> <sup>&dagger;</sup> Note that libraries that have already had SWATHS applied can only be filtered by protein list",
                     'min_num_frags' => "Minimum number of fragment ions to include an assay. <br><br>Must be less than or equal to Max num fragments ",
                     'max_num_frags' => "Maximum number of fragment ions to use in an assay for a specific precursor. <br><br> Must be greater than or equal to Min num fragments ",
                     'basename' => "Base name for exported library files (optional). Default is library name. ",
                     'prec_min_mz' => "Minimum precursor ion m/z value for library entries ",
                     'prec_max_mz' => "Maximum precursor ion m/z value for library entries ",
                     'frag_min_mz' => "Minimum fragment ion m/z value for library entries ",
                     'frag_max_mz' => "Maximum fragment ion m/z value for library entries ",
                       'cmod_mass' => 'Generate transision with heavy-labeled versions of selected amino acids, Use ctrl-shift for multiple options.',
                       'cmod_opts' => $q->escape( 'Generate heavy transitions, light and heavy (L & H), or light only (default).  Relevant only if one or more heavy label options are selected.' ),
                     'swaths_file' => "File of SWATH bins, format is lower mz bound 'tab' upper bound mz 'newline' ",
                     'no_swaths_file' => "SWATH file not needed, ion library filtered at analysis time (Peakview) ",
                     'swath_size' => "Size of each SWATH bin, default is 25 Th ",
                     'swath_overlap' => "Overlap between adjacent SWATH bins, on each side - so 1 Th will result in 2 Th overlap ",
                     'Proteins' => "File of protein accessions, one per line, with which to filter library. One accession space per organism allowed: Human - Uniprot, Mtb - Tuberculist (Rv)",
                     'domain_protein_list_id' => "Set of protein accessions from one of the Human Proteome Project Biology/Disease lists <br> Note that this will only work with Human libraries" );
  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;color: #002664; font-size:150%;font-weight:700" id=heading>
   <font color =#ff5f00 >|</font> Library Download </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/ ) {
        $publication = "<font color = #ff5f00><b>Publication:</b></font> <i>$lib_zero->[14]</i> ($lib_zero->[13]) <br>";
      } else {
        $publication = "<font color = #ff5f00><b>Publication:</b></font> <i>$lib_zero->[14]</i> (<a href='$lib_zero->[13]'>View</a>) <br>";
      }
    }
    my $description = '';
    if ( $lib_zero->[15] ) {
      $description = "<font color = #002664>$lib_zero->[15]</font><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>
	 <font color = #002664>
     <span style="font-family:Barlow, 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
	 </font>
    <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 get_subset_form {

  # Set this to true if we are in the process of downloading a library
  my $custom = ( $params->{action} =~ /trigger/i ) ? '0' : 1;

  # Needed this sooner
  my $swath_overlap = $params->{swath_overlap} || 0;

  my $custom_link = '';
  if ( $custom ) {

    if ( !$params->{library} || $params->{library} !~ /^\d+$/ ) {
     print "<script type='text/javascript'> set_status( 'Missing or illegal library ID' ); </script>" ;
    } else {

      my $format_constraint = '';
      if ( $params->{format} ) {
        $format_constraint = "AND file_format = '$params->{format}'";
      }
      my $sql = qq~
      SELECT file_path, file_format 
      FROM $TBAT_DIA_LIBRARY 
      WHERE dia_library_id = $params->{library}
      AND project_id IN ( $project_ids )
      AND record_status = 'N'
      ~;
      my $sth = $sbeams->get_statement_handle( $sql );
      my $path = '';
      my $format = '';
      while ( my @row = $sth->fetchrow_array() ) {
        $path = $row[0];
        $format = $row[1];
        last;
      }
      if ( !$path || ! -e $path ) {
        print "<script type=text/javascript> set_status( 'Missing library path. If you have an access code please enter it at the bottom of <a href=http://www.swathatlas.org>this page</a>' ); </script>" ;
      } else {
        my $fname = $sbeams->getRandomString( num_chars => 20 );

#        my $exec = "$PHYSICAL_BASE_DIR/lib/scripts/PeptideAtlas/extract_ionlibrary_subset.pl --in $path --out /tmp/$fname --format $format ";
	my $exec = "/proteomics/sw/scripts/extract_ionlibrary_subset.pl --in $path --out /tmp/$fname --format $format ";
        if ( $params->{swaths_file} ) {
          my $file_name = $q->param( 'swaths_file' );
          my $sfile = $sbeams->getRandomString( num_chars => 20 );
          open SWATHS, ">/tmp/$sfile";
          while ( my $line = <$file_name> ) {
            print SWATHS $line;
          }
          close SWATHS;
          $exec .= "--swath /tmp/$sfile ";
        } else {
          $exec .= "--prec_min $params->{prec_min_mz} --prec_max $params->{prec_max_mz} --width $params->{swath_size} --overlap $swath_overlap --print_swaths ";
        }

        $exec .= " --frag_min $params->{frag_min_mz} --frag_max $params->{frag_max_mz} ";

        my $pfile = $sbeams->getRandomString( num_chars => 20 );
        if ( $params->{protein_file} ) {
          my $file_name = $q->param( 'protein_file' );
          open PROTS, ">/tmp/$pfile";
          while ( my $line = <$file_name> ) {
            print PROTS $line;
          }
          close PROTS;
          $exec .= "--protein /tmp/$pfile ";

          # Yeast library has garbage in uniprot_acc field 
          if ( $path =~ /Yeast/i ) {
            $exec .= "--use_protein ";
          }
        } elsif ( $params->{domain_protein_list_id} ) {

          my $sql = qq~;
          SELECT DISTINCT uniprot_accession 
          FROM $TBAT_DOMAIN_PROTEIN_LIST DPL
          JOIN $TBAT_DOMAIN_LIST_PROTEIN DLP
            ON DPL.protein_list_id = DLP.protein_list_id
          WHERE DLP.protein_list_id = $params->{domain_protein_list_id} 
            AND project_id IN ( $project_ids )
          ~;
          my $sth = $sbeams->get_statement_handle( $sql );
          open PROTS, ">/tmp/$pfile";
          while( my @row = $sth->fetchrow_array() ) {
            print PROTS "$row[0]\n";
          }
          $exec .= "--protein /tmp/$pfile ";

          close PROTS;
#        } else {
#          die Dumper( $params );
        }
        $exec .= "--min_num $params->{min_num_frags} ";
        $exec .= "--max_num $params->{max_num_frags} ";

        if ( $params->{cmod_mass} && $params->{cmod_opts} ) {
          $exec .= "--cmod_mass $params->{cmod_mass} --cmod_opts $params->{cmod_opts} ";
        }


        $log->info( $exec );
#        print "<script type=text/javascript> update_status( '<br>$exec' ); </script>" ;
        my @status = `$exec`;
        my $status = join( ' ', @status );
        $status =~ s/\n/\<br\>/gm;
        print "<script type=text/javascript> set_status( 'Finished. <br><br>$status' ); </script>" ;

        if ( -e "/tmp/$fname"  ) {


          # Command finished successfully. 

          my $result = '';
          my $base_name = basename( $path );
          if ( $params->{basename} ) {
            if ( $params->{basename} =~ /.*(\....)$/ ) {
              $base_name = $params->{basename};
            } else {
              my $suffix = ( $base_name =~ /\.txt$/ ) ? '.txt' :
                           ( $base_name =~ /\.csv$/ ) ?'.csv' : '.tsv';
              $base_name = $params->{basename} . $suffix;
            }
            
          }

          my $bs = {};
          move( "/tmp/$fname", "$PHYSICAL_BASE_DIR/tmp/$fname" );
          my $full_fname = "$PHYSICAL_BASE_DIR/tmp/$fname";
          my $tmp_fname = "/tmp/$fname";

          if ( $params->{upload_to_basespace} ) {
            $bs = upload_to_basespace( basename => $base_name, tmpfile_name => $full_fname, status => $status );
          }

#          $base_name =~ s/\.csv/\.tsv/;
#          $base_name =~ s/\.txt/\.tsv/;
          if ( -e "/tmp/$fname.swaths" ) {
            move( "/tmp/$fname.swaths", "$PHYSICAL_BASE_DIR/tmp/" );
            my $swath_file_link = qq~ Download generated <a href=$CGI_BASE_DIR/downloadFile.cgi?raw_download=1;name=swath_windows.txt;format=tsv;tmp_file=$tmp_fname.swaths>SWATH window file</a>.~;
            print "<script type=text/javascript> update_status( '<br>$swath_file_link' ); </script>" ;
          }

          if ( -e "$full_fname" ) {
            $result = qq~ Customized library is ready for download via this <a href=$CGI_BASE_DIR/downloadFile.cgi?raw_download=1;name=$base_name;format=tsv;tmp_file=$tmp_fname>link</a>~;
          } else {
            $result = "Library customization failed";
          }
          print "<script type=text/javascript> update_status( '<br>$result' ); </script>" ;

        }

      }
    }
  }
  
  my $title = qq~

     <br>
      ~;
	  
	  
  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> Custom Library Download </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 a list of proteins to extract a subset SWATH/DIA library. This can be done with a user-uploaded list, or with any of the 
   Biology/Disease-driven Human Proteome Project ( <a href="http://db.systemsbiology.net/devDC/sbeams/cgi/PeptideAtlas/proteinList?protein_list_id=2"> B/D-HPP </a>) contributed lists.
  </div>
  ~;

  my %org2species = ( mtb => 'Mycobacterium tuberculosis',
                      human => 'Homo sapiens',
                      ecoli => 'Eschiera coli',
                      yeast => 'Saccharomyces cerevisie' );

  my %orgs;
  my %inst;
  my $format_constraint =  " AND file_format IN ('peakview', 'openswath', 'mprophet' ) ";
  if ( $params->{format} ) {
    $format_constraint = "AND file_format = '$params->{format}'";
  }
  my $sql = qq~
  SELECT dia_library_id, dia_library_name, file_path, file_format, is_master,
         instrument_type_name
  FROM $TBAT_DIA_LIBRARY DIL 
  JOIN $TBAT_INSTRUMENT_TYPE IT ON IT.instrument_type_id = DIL.instrument_type_id
  WHERE project_id IN ( $project_ids )
  $format_constraint
--  AND is_master = 'Y'
  AND DIL.record_status = 'N' 
  ORDER BY dia_library_tag, dia_library_name 
  ~;
# 0 dia_library_id
# 1 dia_library_name
# 2 DIL.comment
# 3 file_path
# 4 file_format
  my $sth = $sbeams->get_statement_handle( $sql );
  my %libraries; 

  my $lib_select;
  my $lib_size = 0;
  while ( my @row = $sth->fetchrow_array() ) {
    if ( $params->{format} ) {
      next unless $params->{format} =~ /$row[3]/i;
      next if ( $params->{format} =~ /peakview/i && $row[5] =~ /orbi/i );
    }
    $lib_size++;
    my $selected = '';
    if ( $row[0] == $params->{lib_id} ) {
      $selected = 'selected';
    }
    $lib_select .= "<option value=$row[0] $selected > $row[1] </option>\n";
  }
  $lib_size = 4 if $lib_size > 4;
  $lib_select .= "</select>\n";
  $lib_select = "<select size=$lib_size name=library id=library>\n" . $lib_select;

  my $inst_select = "<select name=instrument><option value=''>---</option>";
  for my $inst ( sort( keys( %inst ) ) ) {
    $inst_select .= "<option value='$inst' > $inst </option>\n";
  }
  $inst_select .= "</select>";

  my $sql =<<"  END";
  SELECT title, first_name, last_name, protein_list_id
  FROM $TBAT_DOMAIN_PROTEIN_LIST DPL
  JOIN $TB_CONTACT C ON DPL.owner_contact_id = C.contact_id
  ORDER BY title
  END

  my $title2help = get_help_links();
  my $or = '~or~';

  my $prec_min_mz = $params->{prec_min_mz} || 400;
  my $prec_max_mz = $params->{prec_max_mz} || 1200;
  my $frag_min_mz = $params->{frag_min_mz} || 350;
  my $frag_max_mz = $params->{frag_max_mz} || 1600;
  my $swath_size = $params->{swath_size} || 25;

  my $range = $prec_max_mz - $prec_min_mz;
  my $n_bins = int( $range/$swath_size );
  $n_bins++ if $range/$swath_size > $n_bins;
  my $min_num_frags = $params->{min_num_frags} || 6;
  my $max_num_frags = $params->{max_num_frags} || 6;

  my $domain_protein_list_select = get_protein_list_selector();
  my $spacer = '&nbsp;' x 30;

  my $no_swaths = '';
  if ( $params->{format} && $params->{format} =~ /peakview/i ) {
    $no_swaths = 'checked';
  }

  my $cmod_mass_select = get_cmod_select( $params->{cmod_mass} );
  my $cmod_opts_radio = get_cmod_radio( $params->{cmod_opts} );

  my $form = qq~
  $help
  <br><br>
  <script type='text/javascript'>
  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;
  }
  function specify_swath ( mode ) {
    var prec_min_mz = document.getElementById( 'prec_min_mz' );
    var prec_max_mz = document.getElementById( 'prec_max_mz' );
    var swath_size = document.getElementById( 'swath_size' );
    var swath_overlap = document.getElementById( 'swath_size' );
    var swath_cnt = document.getElementById( 'swath_cnt' );
    if ( mode == 'file' ) {
      prec_min_mz.value = '';
      prec_max_mz.value = '';
      swath_size.value = '';
      swath_overlap.value = '';
      swath_cnt.innerHTML = '';
    } else {
      var swaths_file = document.getElementById( 'swaths_file' );
      swaths_file.value = '';
      var min_val = prec_min_mz.value;
      var max_val = prec_max_mz.value;
      var swath_size_val = swath_size.value
      var swath_overlap_val = swath_overlap.value

      if ( min_val && max_val && swath_size_val ) {
        var range = max_val - min_val;
        var n_bins = parseInt( range/swath_size_val );
        var mod = range % swath_size_val;
        if ( mod > 0 ) {
          n_bins = n_bins + 1;
        }
        swath_cnt.innerHTML = '(' + n_bins + ' total bins)';

      } else {
        swath_cnt.innerHTML = '';
      }
    }
  }
  </script>
  <style type="text/css">
   .cellblock_top { border-top:1px solid; border-color:#002664; border-left:1px solid; border-right:1px solid; padding:10px }
   .cellblock_bottom { border-bottom:thin solid; border-color:#002664; border-left:thin solid; border-right:thin solid; padding:10px }
   .cellblock { border-color:#002664; border-left:thin solid; border-right:thin solid}
   .cellblock_complete { border-color:#002664; border-left:thin solid; border-right:thin solid; border-top: thin solid; border-bottom:thin solid }
  </style>

  <table style="border-collapse: collapse">
  <form method=post id=customize onSubmit="return check_form()" enctype="multipart/form-data">
  <input type=hidden name=mode value=subset_libs />
  <input type=hidden name=action value=download />
  $basespace{basespace_params}
   <tr><td colspan=3 align=left><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading><b>Library selection</b></div></td></tr>
  <tr class=cellblock_top>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Input library</div><sup>&dagger;</sup>:</i></b></td>
    $title2help->{Library}
    <td>$lib_select</td>
  </tr>
  <tr class=cellblock_bottom>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Output file name:</div></i></b></td>
    $title2help->{basename}
    <td><input type=text name=basename id=basename size=36/></td>
  </tr>
  <tr>
    <td colspan=3>&nbsp;</td>
    <tr><td colspan=3 align=left><b><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading>Protein filtering</div></b></td></tr>
  </tr>
  <tr class="cellblock_top">
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Proteins:</div></i></b></td>
    $title2help->{Proteins}
    <td><input type=file name=protein_file id=protein_file></input></td>
  </tr>
  <tr class=cellblock>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td align=left>$or</td>
  </tr>
  <tr class="cellblock_bottom">
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> HPP/BD list:</div></i></b></td>
    $title2help->{domain_protein_list_id}
    <td>$domain_protein_list_select</input></td>
  </tr>
  <tr>
    <td colspan=3>&nbsp;</td>
  </tr>
  <tr><td colspan=3 align=left><b><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading>M/Z filtering</div></b></td></tr>
  <tr class=cellblock_top>
     <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Min precursor mz:</div></i></b></td>
    $title2help->{prec_min_mz}
    <td><input type=text id=prec_min_mz name=prec_min_mz onchange=specify_swath('direct') size=12 value=$prec_min_mz></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> Max precursor mz:</div></i></b></td>
    $title2help->{prec_max_mz}
    <td><input type=text id=prec_max_mz name=prec_max_mz onchange=specify_swath('direct') size=12 value=$prec_max_mz></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> Min fragment mz:</div></i></b></td>
    $title2help->{frag_min_mz}
    <td><input type=text id=frag_min_mz name=frag_min_mz onchange=specify_swath('direct') size=12 value=$frag_min_mz></input></td>
  </tr>
  <tr class=cellblock_bottom>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Max fragment mz:</div></i></b></td>
    $title2help->{frag_max_mz}
    <td><input type=text id=frag_max_mz name=frag_max_mz onchange=specify_swath('direct') size=12 value=$frag_max_mz></input></td>
  </tr>
  <tr>
    <td colspan=3>&nbsp;</td>
  </tr>
  <tr><td colspan=3 align=left><b><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading>Number of fragment ions</div></b></td></tr>

  <tr class=cellblock_top>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Min num fragments:</div></i></b></td>
    $title2help->{min_num_frags}
    <td><input type=text id=min_num_frags name=min_num_frags onchange=check_num_frags() size=12 value=$min_num_frags></input></td>
  </tr>
  <tr class=cellblock_bottom>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Max num fragments:</div></i></b></td>
    $title2help->{max_num_frags}
    <td><input type=text id=max_num_frags name=max_num_frags onchange=check_num_frags() size=12 value=$max_num_frags></input></td>
  </tr>
  <tr>
    <td colspan=3>&nbsp;</td>
  </tr>

  <tr><td colspan=3 align=left><b><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading>Isotopic labelling</div></b></td></tr>

  <tr class=cellblock_top>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Heavy isotopes:</div></i></b></td>
    $title2help->{cmod_mass}
    <td>$cmod_mass_select</td>
  </tr>
  <tr class=cellblock_bottom>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> Transition types:</div></i></b></td>
    $title2help->{cmod_opts}
    <td>$cmod_opts_radio</td>
  </tr>
  <tr>
    <td colspan=3>&nbsp;</td>
  </tr>

  <tr><td colspan=3 align=left><b><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading>SWATH Settings</div></b></td></tr>

  <tr class="cellblock_top">
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading>Upload SWATHs file:</div></i></b></td>
    $title2help->{swaths_file}
    <td><input type=file name=swaths_file id=swaths_file onchange=specify_swath('file')></input></td>
  </tr>
  <tr class=cellblock>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td align=left>$or</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>No SWATHs file:</div></b></td>
    $title2help->{no_swaths_file}
    <td align=left><input type=checkbox $no_swaths /></td>
  </tr>
  <tr class=cellblock>
    <td>&nbsp;</td>
    <td>&nbsp;</td>
    <td align=left>$or</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> SWATH window size:</div></i></b></td>
    $title2help->{swath_size}
    <td white-space:nowrap><input type=text name=swath_size id=swath_size onchange=specify_swath('direct') size=12 value=$swath_size></input><span id=swath_cnt>($n_bins total bins)</span></td>
  </tr>
  <tr class=cellblock_bottom>
    <td align=right><b><i><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading> SWATH window overlap:</div></i></b></td>
    $title2help->{swath_overlap}
    <td white-space:nowrap><input type=text name=swath_overlap id=swath_overlap onchange=specify_swath('direct') size=12 value=$swath_overlap></input></td>
  </tr>
  <tr>
    <td colspan=3>&nbsp;</td>
  </tr>


  <tr>
    <td>&nbsp;</td>
    <td colspan=2 align=left><div style="font-family:Barlow, Arial, sans-serif;color: #002664; font-size:100%;font-weight:700" id=heading><input type=submit value='Generate Custom Library'></input></div></td>
	
  </tr>
  </table>
  
  </form>
  <script type="text/javascript">
  function check_form() {
    var prec_min_mz = document.getElementById( 'prec_min_mz' );
    var prec_max_mz = document.getElementById( 'prec_max_mz' );
    var swath_size = document.getElementById( 'swath_size' );
    var swath_cnt = document.getElementById( 'swath_cnt' );
    var swaths_file = document.getElementById( 'swaths_file' );
    var library = document.getElementById( 'library' );

    var min_val = prec_min_mz.value;
    var max_val = prec_max_mz.value;
    var swath_size_val = swath_size.value

//    if ( library.selectedIndex  ) {
//      alert( library.selectedIndex.value );
//      return false;
//    }
//    alert( typeof( library.selectedIndex ) );

    var status = true;
    if ( min_val && max_val && swath_size_val ) {
      status = true;
    }
    if ( swaths_file.value ) {
      status = true;
    }
    if ( ! status ) {
      alert( "Must provide either a SWATH file, or all of min, max, and SWATH window size" );
    }
    var min_frags = document.getElementById( 'min_num_frags' );
    var max_frags = document.getElementById( 'max_num_frags' );
    if ( parseInt(min_frags.value) > parseInt(max_frags.value) ) {
      alert( "Min frags cannot be less than Max frags ");
      status = false;
    }

    return status;
  }
  </script>
    <br>
  <br>
  ~;

  return $form;
}

sub process_params {
  my $params = {};
  $sbeams->parse_input_parameters( q => $q, parameters_ref => $params );
  $sbeams->processStandardParameters( parameters_ref => $params );
  return( $params );
}

sub get_cmod_select {
  
  my $curr_val = shift || '';
  my %sel = ( K8 => '', R10 => '', K6 => '', R6 => '' );
  my %seen;
  for my $curr ( split( ',', $curr_val ) ) {
    $sel{$curr} = 'SELECTED';
  }

  my $cmod_sel = qq~
    <SELECT SIZE=4 MULTIPLE NAME=cmod_mass>
      <OPTION VALUE='' ></OPTION>
      <OPTION VALUE=K8 $sel{K8}>Lysine + 8</OPTION>
      <OPTION VALUE=R10 $sel{R10}>Arginine + 10</OPTION>
      <OPTION VALUE=K6 $sel{K6}>Lysine + 6</OPTION>
      <OPTION VALUE=R6 $sel{R6}>Arginine + 6</OPTION>
    </SELECT>
  ~;
  return $cmod_sel;
}

sub get_cmod_radio {
  my $curr_val = shift || 'light_only';
  my %sel = (  light_only => '', 'heavy_only' => '', both => '' );
  $sel{$curr_val} = 'checked';

  my $cmod_radio = qq~
  <INPUT TYPE=radio name=cmod_opts $sel{light_only} value=light_only> Light only </INPUT>
  <INPUT TYPE=radio name=cmod_opts $sel{heavy_only} value=heavy_only> Heavy only </INPUT>
  <INPUT TYPE=radio name=cmod_opts $sel{both} value=both> L & H </INPUT>
  ~;
  return $cmod_radio;
}



sub authenticate_to_basespace {

  my $uri = $basespace{appsessionuri};
  my @appsession = split( /\//, $uri );
  my $appsession_id = $appsession[$#appsession];
  $basespace{appsession_id} = $appsession_id;

  # Have we been through authentication in this page?
  if ( $basespace{access_token} ) {
#    $log->info( "Already authenticated, returning" );
    return;
  }

  # Will need a new user agent for subsequent transactions
  my $ua = LWP::UserAgent->new();
  $ua->cookie_jar( {} );

  # Is there a cached value?
  my $token = $sbeams->getSessionAttribute( key => $basespace{appsessionuri} );

  if ( $token ) {   # Yes, will use to set header
#    $log->info( "Fetched token from Session Cookie" );

  } else { # No, fetch from bs using client ids and auth_code

    my $client = $CONFIG_SETTING{BASESPACE_IONLIBRARY_CLIENT_ID} || '';
    my $client_secret = $CONFIG_SETTING{BASESPACE_IONLIBRARY_CLIENT_SECRET_ID} || '';
    my $redirect = "https://db.systemsbiology.net" . $HTML_BASE_DIR . '/cgi/PeptideAtlas/GetDIALibs';

    my $auth_code = $basespace{authorization_code};

    my $auth_url = 'https://api.basespace.illumina.com/v1pre3/oauthv2/token';
    my $post_param_ref = { client_id => $client,
                       client_secret => $client_secret, 
                                code => $auth_code, 
                        redirect_uri => $redirect, 
                          grant_type => 'authorization_code' };

    my $response = $ua->post( $auth_url, $post_param_ref );

    for my $line ( split( "\n", $response->content() ) ) {
      if ( $line =~ /"access_token":"([^"]+)"/ ) {
        $token = $1;
        last;
      }
    }
  }

  if ( !$token ) {
    $log->warn( "Unable to get authorization from Base Space" );
  } else {

    # Place access token in default header for user agent
    # for all subsequent transactions.
    $ua->default_header( 'x-access-token' => $token );
    $basespace{ua} = $ua;
    $basespace{token} = $token;

    # Cache token for subsequent cgi calls with this appsession
    $sbeams->setSessionAttribute( key => $basespace{appsessionuri}, value => $token );
  }

} # End authenticate_to_basespace

# Fetch appsession info, includes project name and ID to write to
sub get_appsession_properties {

  if ( !$basespace{access_token} ) {
    authenticate_to_basespace();
  } 

  # User Agent created during authentication
  my $ua = $basespace{ua} || return;

  my $appsession_url = $basespace{appsession_url} || 'https://api.basespace.illumina.com/' . $basespace{appsessionuri};
  $basespace{appsession_url} ||= $appsession_url;

  my $response = $ua->get( $appsession_url );
  my @content = $response->content();
  my $appsession = $json->decode( $content[0] );
  $basespace{appsession} = $appsession;

  # Fetch project_id from Response->Properties, as per Illumina. 
  # Response->References also contains info, but is deprecated.
  if ( $appsession->{Response} ) {
    if ( $appsession->{Response}->{Properties} ) {
      for my $ref ( @{$appsession->{Response}->{Properties}->{Items}} ) {
        my $name = $ref->{Name};
        $name =~ s/Input\.//;
        if ( $ref->{Name} eq 'Input.project-id' ) {
          $basespace{project} = $ref->{Content}->{Name};
          $basespace{project_id} = $ref->{Content}->{Id};
        } else {
          $basespace{$name} = $ref->{Content};
        }
      }
    }
  }
#  $basespace{ua} = '';
#  $basespace{appsession} = '';
#  die Dumper( %basespace );

} # End get_appsession_properties


sub upload_to_basespace {

  my %args = @_;

  my $tmp_file = $args{tmpfile_name} || "$PHYSICAL_BASE_DIR/tmp/$params->{tmp_file}";

  # If we came from basespace, are downloading an entire peakview file:
  if (  $params->{format} &&  $params->{format} =~ /peakview/i && $params->{name} &&  $params->{tmp_file} ) {
    $params->{name} =~ s/.csv$/.txt/;
    $params->{name} =~ s/.tsv$/.txt/;
  }
  my $basename = $args{basename} || $params->{name};

  if ( $basename !~ /\.txt$/ ) {
    $basename =~ s/\....$/.txt/;
  }
  if ( $basename !~ /\.txt$/ ) {
    $basename .= '.txt';
  }

  my $status = $args{status} || '';

  if ( ! -e $tmp_file ) {
    die "No tmp file $tmp_file";
    $log->warn( "Missing file $tmp_file" );
    return;
  }

  if ( !$basespace{appsession} ) {
    get_appsession_properties();
  }
#  set_appsession_status( 'Running' );

  my $project = $basespace{project};
  my $project_id = $basespace{project_id};
  my $appsessionuri = $basespace{appsessionuri};
  my $appsession_id = $basespace{appsession_id};
  my $ua = $basespace{ua};
  my $token = $basespace{token};
  if ( !$token ) {
    $basespace{ua} = '';
    $basespace{appsession} = '';
    die Dumper( %basespace );
  }

  if ( $project_id && $project ) {

    # We will assume that no App Results called 'SWATHIonLibraries' exists
    # for this project. Try to create.
    # Required info: Project.Id, AppResult.Name, .Desc, AppSession.ID 
    $basespace{ua} = '';
    $basespace{appsession} = '';

    my $appresult_url = "https://api.basespace.illumina.com/v1pre3/projects/$project_id/appresults";
#    my $appresult_param_ref = { Name => 'SWATHAtlasIonLibraries.txt',
    my $appresult_param_ref = { Name => $basename,
                                Description => "Ion Library $basename from SWATH Atlas for SWATH Analysis",
                                HrefAppSession => $appsessionuri
                              };

    my $ar_result = $ua->post( $appresult_url, $appresult_param_ref );
    my @content = $ar_result->content();
    my $ar_object = $json->decode( $content[0] );
    my $HrefFiles = $ar_object->{Response}->{HrefFiles} || die Dumper( $ar_object );

    # TODO validate ar_result?
    # We have a project, and have created an AppResult. Now upload file

#    $log->info( join( "\t", qw( Auth_code URI Token AppResult Project Project_name basename tmp_file client client_secret ) ) );
#    $log->info( join( "\t", $auth_code, $appsession_id, $token, 'AppResultId', $project_id, $project, $basename, $tmp_file, $client, $client_secret  ) );

    print_js_status( "Uploading file to Base Space, may take a minute or two. <br>" );
    my $t0 = time();

    upload_file_multipart( token => $token, tmp_file => $tmp_file, href => $HrefFiles, name => $basename );
#    upload_file( token => $token, tmp_file => $tmp_file, href => $HrefFiles, name => $basename );

    my $t1 = time();
    my $tdelta = $t1 - $t0;

    # Set analysis Status to Complete
    set_appsession_status( 'Complete', $status );

#    if ( $params->{mode} eq 'download_libs' ) {
#      print_js_status( "Finished upload <br><br>", 1 );
#    }
    print_js_status( "File $basename uploaded to project $project in Base Space in $tdelta seconds<br>" );
    print_js_status( "Returning to Base Space...<br>" );
    sleep 4;
    js_redirect( "https://basespace.illumina.com/analyses/$appsession_id/files" );
    sleep 4;

  } else {
    print_js_status( "<br>Failure: no Base Space projects to write to" );
    return;
  }

}  # End upload_to_basespace

sub upload_file {
  my %args = @_;
  my $token = $args{token};
  my $tmp_file = $args{tmp_file};
  my $basename = $args{name};
  my $HrefFiles = $args{href};

#    my $exe = "curl -v -H 'x-access-token: $token' -d '\@$tmp_file' -H 'Content-Type: text/tab-separated-values' 'https://api.basespace.illumina.com/" . $HrefFiles . "?name=$basename'";
    my $exe = "curl -v -H 'x-access-token: $token' -d '\@$tmp_file' -H 'Content-Type: application/octet-stream' 'https://api.basespace.illumina.com/" . $HrefFiles . "?name=$basename'";
    my @result = `$exe`;
#    $log->info( $exe );
#    $log->info( join( "\n", @result ) );
}


#curl -H 'x-access-token: 20dd0ed0340942a49a5b938a592b6900' -H 'Content-Type: text/tab-separated-values' -X POST https://api.basespace.illumina.com/v1pre3/appresults/16026018/files?name=Frankenfile\&multipart=true

#curl -H 'x-access-token: 20dd0ed0340942a49a5b938a592b6900' -H 'Content-Type: text/tab-separated-values' -X POST -T /tmp/20_parts00 -X PUT https://api.basespace.illumina.com/v1pre3/files/16026108/parts/1

#curl -H 'x-access-token: 20dd0ed0340942a49a5b938a592b6900'  -X PUT https://api.basespace.illumina.com/v1pre3/files/998044314?uploadstatus=Complete


sub upload_file_multipart {
  my %args = @_;
  my $token = $args{token};
  my $tmp_file = $args{tmp_file};
  my $basename = $args{name};
  my $HrefFiles = $args{href};

# /v1pre3/appresults/XXXXX/files/;
  my $parts_href = $HrefFiles;
  $parts_href =~ s/\/files/\/parts/;
  $parts_href =~ s/\/appresults/\/files/;

  my $finish_href = $HrefFiles;
  $finish_href =~ s/\/files//;
  $finish_href =~ s/\/appresults/\/files/;

  my $rdir = $sbeams->getRandomString( num_chars => 20 );
  `mkdir /tmp/$rdir/`;
  `split -b10000000 -d $tmp_file /tmp/$rdir/upload_ `;

   # Initiate upload 
   my $exe = "curl -H 'x-access-token: $token' -H 'Content-Type: text/tab-separated-values' -X POST https://api.basespace.illumina.com/$HrefFiles?name=$basename" . '\&multipart=true';
   my @results = `$exe`;
#   $log->info( "started multipart upload" );
#   $log->info( $exe );
#   $log->info( $results[0] );
    
   my $multipart_upload = $json->decode( $results[0] );
   my $upload_href = $multipart_upload->{Response}->{Href};

   # Upload the parts
   opendir DIR, "/tmp/$rdir/";
   my @files = sort( grep( !/\./, readdir DIR ) );
   my $part = 1;
   for my $file ( @files ) {
     if ( -e $file  ) {
#       $log->info( $file . " exists" );
     }
     $exe = "curl -H 'x-access-token: $token' -H 'Content-Type: text/tab-separated-values' -X POST -T /tmp/$rdir/$file -X PUT https://api.basespace.illumina.com/$upload_href/parts/$part";
#    $log->info( $exe );
     @results = `$exe`;
#     $log->info( "uploaded part $part" );
#     $log->info( join( "\n", @results ) );
     $part++;
   }

   # Finish upload
# curl -H 'x-access-token: 20dd0ed0340942a49a5b938a592b6900'  -X POST https://api.basespace.illumina.com/v1pre3/files/998044314?uploadstatus=Complete
   $exe = "curl -H 'x-access-token: $token' -X POST https://api.basespace.illumina.com/$upload_href?uploadstatus=complete";
   @results = `$exe`;
#   $log->info( $exe );
#   $log->info( "finished multipart upload" );
#   $log->info( join( "\n", @results  ) );
   `rm -Rf /tmp/$rdir/`;

}

sub set_appsession_status {

  my $new_status = shift || return;
  my $status_description = shift || '';
  $status_description =~ s/<br>//gi;

  if ( !$basespace{ua} ) {
    authenticate_to_basespace();
  } 

  my $ua = $basespace{ua};

  my $appsession_url = $basespace{appsession_url};
  $ua->post( $appsession_url, [ Status => $new_status, Statussummary => $status_description ] );
  $ua->post( "$appsession_url/properties", [ 'Logs.tail' => $status_description ] );
  $ua->post( "$appsession_url/properties", [ 'Logs' => $status_description ] );
#  die "$appsession_url/properties";

}

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;
  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] ) ? 
               ( $row[3] =~ /^PXD/ ) ? "<a href='http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$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' );

      $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] };
    }
  }

  if ($params->{output_format} eq 'json') {
    use JSON;
    my $json = new JSON;
    my $jstr = $json->utf8->encode(\%sets);
    print("Access-Control-Allow-Origin: *\n");
    print("Content-Type: application/json\n\n");
    print $jstr;
    return;
  }

#  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__