#!/usr/local/bin/perl ############################################################################### # Program : main.cgi # Author : Eric Deutsch # $Id$ # # Description : This script authenticates the user, and then # displays the opening access page. # # SBEAMS is Copyright (C) 2000-2005 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. # ############################################################################### ############################################################################### # Set up all needed modules and objects ############################################################################### use strict; use Getopt::Long; use FindBin; #use CGI; use lib "$FindBin::Bin/../../lib/perl"; use vars qw ($sbeams $sbeamsMOD $q $current_contact_id $current_username %hash_to_sort $PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $DATABASE $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME @MENU_OPTIONS ); use SBEAMS::Connection qw($q $log); use SBEAMS::Connection::Settings; use SBEAMS::Connection::Tables; use SBEAMS::Connection::TabMenu; use SBEAMS::Connection::DataTable; use SBEAMS::Ontology::Tables; use SBEAMS::Ontology::TableInfo; use SBEAMS::Immunostain; use SBEAMS::Immunostain::Settings; use SBEAMS::Immunostain::Tables; #$q = new CGI; $sbeams = new SBEAMS::Connection; $sbeamsMOD = new SBEAMS::Immunostain; $sbeamsMOD->setSBEAMS($sbeams); my (%CYTSAMPLEHASH, %IMMUNOSPECHASH ); my $subDir = $SBEAMS_SUBDIR; my ($SBEAMS_CY_SUBDIR) = $subDir =~s/Immunostain/Cytometry/; ############################################################################### # Set program name and usage banner for command like use ############################################################################### $PROG_NAME = $FindBin::Script; $USAGE = < \&displayIntro, $START => \&displayMain, $ANTIBODY => \&processAntibody, $STAIN => \&processStain, $CELL => \&processCells, $ERROR => \&processError ); main(); exit(0); ### sub main { # run SBEAMS authentication and exit if a username is not returned exit unless ($current_username = $sbeams->Authenticate( permitted_work_groups_ref => ['Immunostain_user', 'Immunostain_admin', 'Immunostain_readonly', 'Admin'], allow_anonymous_access => 1, # Allows guest without username and password )); # $sbeams->printCGIParams( $q ); # Read in the default input parameters my %parameters; $sbeams->parse_input_parameters( q => $q, parameters_ref => \%parameters); $sbeams->processStandardParameters(parameters_ref=>\%parameters); #### Decide what action to take based on information so far if ($parameters{action} eq "_processCells") { # special handling processCells(ref_parameters=>\%parameters); } else { # normal handling for anything else $sbeamsMOD->display_page_header(); } handle_request(ref_parameters=>\%parameters); $sbeamsMOD->printPageFooter(); } # end main sub handle_request { my %args = @_; # Process the arguments list my $ref_parameters = $args{'ref_parameters'} || die "ref_parameters not passed"; my %parameters = %{$ref_parameters}; # Define some generic varibles my ($i,$element,$key,$value,$line,$result,$sql); my @rows; $current_contact_id = $sbeams->getCurrent_contact_id(); # Show current user context information $sbeams->printUserContext(); my $project_id = $sbeams->getCurrent_project_id(); # If the current user is not the owner, the check that the # user has privilege to access this project if ($project_id > 0) { my $best_permission = $sbeams->get_best_permission(); # If not at least data_reader, set project_id to a bad value $project_id = -99 unless ($best_permission > 0 && $best_permission <=40); } my $cytoSql = "select fcs_run_id, substring(sample_name,0,7) from $TBCY_FCS_RUN"; my $immunoSql = "select specimen_name, specimen_id from $TBIS_SPECIMEN"; %CYTSAMPLEHASH = $sbeams->selectTwoColumnHash($cytoSql); %IMMUNOSPECHASH = $sbeams->selectTwoColumnHash($immunoSql); foreach my $key (keys %IMMUNOSPECHASH) { if ($CYTSAMPLEHASH{$key}) { $IMMUNOSPECHASH{$key} = 1 } else { $IMMUNOSPECHASH{$key} = 0 } } my $action = $parameters{'action'}; my $sub = $actionHash{$action} || $actionHash{$INTRO}; # If the project_id wasn't reverted to -99, display information about it if ($project_id == -99) { print <<" END_WARNING"; You do not have access to this project, please contact the owner, if you want to have access. END_WARNING } else { &$sub(ref_parameters=>\%parameters,project_id=>$project_id); } } sub displayIntro { my %args = @_; #data for the grand summary #/*total number of stains*/ my $totalStainsSql = qq /select count(*) from $TBIS_ASSAY/; #/*number of imaged stains*/ my $imagedStainsSql = qq/ select assay_name from $TBIS_ASSAY ss join $TBIS_ASSAY_CHANNEL ac on ss.assay_id = ac.assay_id join $TBIS_ASSAY_IMAGE si on ac.assay_channel_id = si.assay_channel_id group by assay_name/; #/*number of char. stains*/ my $charStainsSql = qq/ select assay_name from $TBIS_ASSAY ss join $TBIS_ASSAY_CHANNEL ac on ss.assay_id = ac.assay_id join $TBIS_ASSAY_UNIT_EXPRESSION scp on ac.assay_channel_id = scp.assay_channel_id group by assay_name/; #/*total number of antibodies*/ my $totalAntibodySql = qq / select count(*) from $TBIS_ANTIBODY/; #/*number of characterized anitbodies*/ my $charAntibodySql = qq / select antibody_name from $TBIS_ASSAY ss join $TBIS_ASSAY_CHANNEL ac on ss.assay_id = ac.assay_id join $TBIS_ASSAY_UNIT_EXPRESSION scp on ac.assay_channel_id = scp.assay_channel_id join $TBIS_ANTIBODY ab on ac.antibody_id = ab.antibody_id group by antibody_name/; #/*total number of antibodies*/ my $totalProbeSql = qq / select count(*) from $TBIS_PROBE/; #number of characterized probes my $charProbeSql = qq / select probe_name from $TBIS_ASSAY ss join $TBIS_ASSAY_CHANNEL ac on ss.assay_id = ac.assay_id join $TBIS_ASSAY_UNIT_EXPRESSION scp on ac.assay_channel_id = scp.assay_channel_id join $TBIS_PROBE p on ac.antibody_id = p.probe_id group by probe_name/; #/*total number of images*/ my $totalImagesSql = qq / select count(*) from $TBIS_ASSAY_IMAGE/; #/*number of unique images */ my $uniqueImagesSql = qq / select assay_image_id from $TBIS_ASSAY_IMAGE where patindex('%- %', image_name) != 0/; my $ctitle = ''; my $totalStains =($sbeams->selectOneColumn($totalStainsSql))[0]; my $imagedStains = scalar($sbeams->selectOneColumn($imagedStainsSql)); my $charStains = scalar($sbeams->selectOneColumn($charStainsSql)); my $totalAntibody = ($sbeams->selectOneColumn($totalAntibodySql))[0]; my $charAntibody = scalar($sbeams->selectOneColumn($charAntibodySql)); my $totalImages = ($sbeams->selectOneColumn($totalImagesSql))[0]; my $uniqueImages = scalar($sbeams->selectOneColumn($uniqueImagesSql)); #not used my $totalProbe = ($sbeams->selectOneColumn($totalProbeSql))[0]; my $charProbe = scalar($sbeams->selectOneColumn($charProbeSql)); $log->warn( "UNIQ: $uniqueImagesSql => $uniqueImages " ); $log->warn( "STAI: $imagedStainsSql => $imagedStains" ); # get the project id my $project_id = $args{'project_id'} || die "project_id not passed"; #load the javascript functions #get the tissue and the organisms for this project and display them as check boxes my $organismSql = qq~ select s.organism_id,organism_name from $TBIS_SPECIMEN s join $TB_ORGANISM sdo on s.organism_id = sdo.organism_id WHERE s.project_id = '$project_id' group by organism_name,s.organism_id ~; my %organismHash = $sbeams->selectTwoColumnHash($organismSql); #get all the data (specimen, stains, slides) for this project and display the data my %tissueHash = getTissueHash( $project_id ); checkGO( \%tissueHash ); my $sql = qq~ select sp.specimen_id, ss.assay_id ,si.assay_image_id,sbo.organism_name,tt.tissue_type_name,sb.specimen_block_id, sbo.organism_id,tt.tissue_type_id from $TBIS_ASSAY ss left join $TBIS_SPECIMEN_BLOCK sb on ss.specimen_block_id = sb.specimen_block_id left join $TBIS_SPECIMEN sp on sb.specimen_id = sp.specimen_id left join $TBIS_TISSUE_TYPE tt on sp.tissue_type_id = tt.tissue_type_id left join $TB_ORGANISM sbo on sp.organism_id = sbo.organism_id LEFT JOIN $TBIS_ASSAY_CHANNEL ac ON ss.assay_id = ac.assay_id left join $TBIS_ASSAY_IMAGE si on ac.assay_channel_id = si.assay_channel_id WHERE SP.project_id = '$project_id' order by Organism_Name ~; my @rows = $sbeams->selectSeveralColumns($sql); # If there are experiments, display them my (%hash,%stainedSlideHash,%imageHash,%tissueTypeHash); my %organism_ids; my %tissue_type_ids; my $pad = '  '; my $cprojHTML = ''; my $summaryHTML = ''; #we got some data for this project if (@rows) { foreach my $row (@rows) { my ($specimenID,$stainedSlideID,$slideImageID,$organismName,$tissueName,$specimenBlockID,$organism_id,$tissue_type_id) = @{$row}; $organism_ids{$organismName} = $organism_id; $tissue_type_ids{$tissueName} = $tissue_type_id; $hash{$organismName}->{specimenID}->{count}++ if ($specimenID and !exists($hash{$organismName}->{specimenID}->{$specimenID})); $hash{$organismName}->{stainedSlideID}->{count}++ if ($stainedSlideID and !exists($hash{$organismName}->{stainedSlideID}->{$stainedSlideID})); $hash{$organismName}->{slideImageID}->{count}++ if ($slideImageID and !exists($hash{$organismName}->{slideImageID}->{$slideImageID})); $hash{$organismName}->{specimenID}->{$specimenID} = 1; $hash{$organismName}->{stainedSlideID}->{$stainedSlideID} = 1; $hash{$organismName}->{slideImageID}->{$slideImageID} = 1; $hash{$organismName}->{specimenBlockID}->{$specimenBlockID} = 1 if $specimenBlockID; $tissueTypeHash{$tissueName}->{$organismName}->{specimenID}->{count}++ if ($specimenID and !exists($tissueTypeHash{$tissueName}->{$organismName}->{specimenID}->{$specimenID})); $tissueTypeHash{$tissueName}->{$organismName}->{stainedSlideID}->{count}++ if ($stainedSlideID and !exists($tissueTypeHash{$tissueName}->{$organismName}->{stainedSlideID}->{$stainedSlideID})); $tissueTypeHash{$tissueName}->{$organismName}->{slideImageID}->{count}++ if ($slideImageID and !exists($tissueTypeHash{$tissueName}->{$organismName}->{slideImageID}->{$slideImageID})); $tissueTypeHash{$tissueName}->{$organismName}->{specimenID}->{$specimenID} = 1; $tissueTypeHash{$tissueName}->{$organismName}->{stainedSlideID}->{$stainedSlideID} = 1; $tissueTypeHash{$tissueName}->{$organismName}->{slideImageID}->{$slideImageID} = 1; $tissueTypeHash{$tissueName}->{$organismName}->{specimenBlockID}->{$specimenBlockID} = 1 if $specimenBlockID; } my $mouseString = join ', ', keys %{$hash{Mouse}->{specimenBlockID}}; my $humanString = join ', ', keys %{$hash{Human}->{specimenBlockID}}; my $mouseBladderString = join ', ', keys %{$tissueTypeHash{Bladder}->{Mouse}->{specimenBlockID}}; my $humanBladderString = join ', ', keys %{$tissueTypeHash{Bladder}->{Human}->{specimenBlockID}}; # New render layer, 12-23-2004 my $title_proto = 'TITLEHERE:'; ( my $stitle = $title_proto ) =~ s/TITLEHERE/Immunostain data in project/; ( my $otitle = $title_proto ) =~ s/TITLEHERE/Summary by Organism/; ( my $ttitle = $title_proto ) =~ s/TITLEHERE/Summary by Tissue Type/; ( $ctitle = $title_proto ) =~ s/TITLEHERE/Custom Summary/; $summaryHTML =<<" END_SUMMARY"; $stitle
END_SUMMARY my $overviewTable = SBEAMS::Connection::DataTable->new( BORDER => 0 ); $overviewTable->addRow( [$stitle] ); $overviewTable->setCellAttr( ROW => 1, COL => 2, COLSPAN => 2, ALIGN => 'LEFT' ); $overviewTable->addRow( ["$pad Total Number of Immunohistochemical (IHC) Stains:", $totalStains] ); $overviewTable->addRow( ["$pad Number of characterized IHC Stains:", $charStains] ); $overviewTable->addRow( ["$pad Number of IHC Stains with Images:", $imagedStains] ); $overviewTable->addRow( ["$pad Total Number of Antibodies:", $totalAntibody] ); $overviewTable->addRow( ["$pad Number of Antibodies with Tissue Characterization:", $charAntibody] ); $overviewTable->addRow( ["$pad Total Number of Images (includes magnified views of identical Samples):", $totalImages] ); $overviewTable->addRow( ["$pad Total Number of distinct Images (distinct Images of different Samples):", $uniqueImages] ); $overviewTable->setColAttr( ROWS => [1..$overviewTable->getRowNum()], COLS => [ 2 ], ALIGN => 'RIGHT', NOWRAP => 1 ); # print $summaryHTML; $summaryHTML = "
$overviewTable
"; my $summarytable = SBEAMS::Connection::DataTable->new( BORDER => 0, CELLSPACING => 1, CELLPADDING => 1 ); $summarytable->addRow( [ ' ', '# Specimens', '# Stains', '# Images', ' ' ] ); # Store rows with titles so we can apply formatting later my @titlerows; $summarytable->addRow( [$otitle] ); my @trow; foreach my $key (sort keys %hash) { # Loop through organism summary my $help = "Show expression summary for $key tissue samples for each CD"; my $cgiparams = join( ';', 'action=QUERYHIDE', "organism_id=$organism_ids{$key}", 'display_options=MergeLevelsAndPivotCellTypes' ); my $link = <<" END"; [Immunostain Summary] END # undef is not a number! for ( qw( specimenID stainedSlideID slideImageID ) ) { $hash{$key}->{$_}->{count} ||= 0; } @trow = ( "$key  ", $hash{$key}->{specimenID}->{count}, $hash{$key}->{stainedSlideID}->{count}, $hash{$key}->{slideImageID}->{count}, $link ); $summarytable->addRow( \@trow ); } # end organism loop $summarytable->addRow( [$ttitle] ); push @titlerows, $summarytable->getRowNum(); foreach my $key (sort keys %tissueTypeHash) { # Loop through tissue types foreach my $org (sort keys %hash) { my $help = "Display expression summary for $org $key samples for each CD"; # undef is not a number! for ( qw( specimenID stainedSlideID slideImageID ) ) { $tissueTypeHash{$key}->{$org}->{$_}->{count} ||= 0; } my $cgiparams = join( ';', 'action=QUERYHIDE', "tissue_type_id=$tissue_type_ids{$key}", "organism_id=$organism_ids{$org}", "display_options=MergeLevelsAndPivotCellTypes" ); my $link =<<" END_LINK"; [Immunostain Summary] END_LINK @trow = ( "$org $key  ", $tissueTypeHash{$key}->{$org}->{specimenID}->{count}, $tissueTypeHash{$key}->{$org}->{stainedSlideID}->{count}, $tissueTypeHash{$key}->{$org}->{slideImageID}->{count}, $link ); $summarytable->addRow( \@trow ); } } # End tissue type loop $summarytable->setColAttr( ROWS => [1..$summarytable->getRowNum()], COLS => [ 1 ], ALIGN => 'RIGHT', NOWRAP => 1 ); $summarytable->setColAttr( ROWS => [1..$summarytable->getRowNum()], COLS => [ 2..4 ], ALIGN => 'CENTER' ); $summarytable->setColAttr( ROWS => [1..$summarytable->getRowNum()], COLS => [ 5 ], ALIGN => 'LEFT', NOWRAP => 1 ); $summarytable->setColAttr( ROWS => \@titlerows, COLS => [ 1 ], COLSPAN => 5, ALIGN => 'LEFT' ); $cprojHTML = "$summarytable"; # $log->debug( "$summarytable" ); #end of if data was found for this project } else { #no data was found $cprojHTML =<<" END_MESSAGE"; $pad This project contains no IHC data
END_MESSAGE } # Create new tabmenu item. This may be a $sbeams object method in the future. my $tabmenu = SBEAMS::Connection::TabMenu->new( cgi => $q ); # Preferred way to add tabs. label is required, helptext optional $tabmenu->addTab( label => 'Current Project', helptext => 'View details of current Project' ); $tabmenu->addTab( label => 'My Projects', helptext => 'View all projects owned by me' ); $tabmenu->addTab( label => 'Recent Resultsets', helptext => 'View recent SBEAMS resultsets' ); $tabmenu->addTab( label => 'Accessible Projects', helptext => 'View projects I have access to' ); # conditional block to exec code based on selected tab. Can define based # on tag label... my $content = ''; if ( $tabmenu->getActiveTabName() eq 'Recent Resultsets' ){ $content = $sbeams->getRecentResultsets() ; } elsif ( $tabmenu->getActiveTab() == 1 ){ ########################################################################## #### Print out project detail stuff, if current or default project exists my $project_id = $sbeams->getCurrent_project_id(); if ( $project_id ) { $content = $sbeams->getProjectDetailsTable( project_id => $project_id ); } # or exec code based on tab index. Tabs are indexed in the order they are # added, starting at 1. } elsif ( $tabmenu->getActiveTab() == 2 ){ ########################################################################## #### Print out all projects owned by the user $content = $sbeams->getProjectsYouOwn(); } elsif ( $tabmenu->getActiveTab() == 4 ){ ########################################################################## #### Print out all projects user has access to $content = $sbeams->getProjectsYouHaveAccessTo(); } # The stringify method is overloaded to call the $tabmenu->asHTML method. # This simplifies printing the object in a print block. if ( $tabmenu->getActiveTab() == 1 ) { my $cb = getCheckboxes( \%organismHash, \%tissueHash ); $content .=<<" END"; $summaryHTML $cprojHTML
END } # Add content to tabmenu (if desired). $tabmenu->addContent( $content ); print "

$tabmenu"; return; } sub displayMain { my %args = @_; my $ref_parameters = $args{'ref_parameters'} || die "ref_parameters not passed"; my %parameters = %{$ref_parameters}; #### Process the arguments list my $project_id = $args{'project_id'} || die "project_id not passed"; # foreach my $k (keys %parameters) # { # print "$k ==== $parameters{$k}
"; # } #populate tbe option list based on what the user checked on the intro page my $antibodySql = "select ab.antibody_id, ab.antibody_name from $TBIS_ANTIBODY ab join $TBIS_ASSAY_CHANNEL ac on ab.antibody_id = ac.antibody_id join $TBIS_ASSAY ss on ac.assay_id = ss.assay_id join $TBIS_SPECIMEN_BLOCK sb on ss.specimen_block_id = sb.specimen_block_id join $TBIS_SPECIMEN s on sb.specimen_id = s.specimen_id join $TBIS_TISSUE_TYPE tt on s.tissue_type_id = tt.tissue_type_id join $TB_ORGANISM sbo on s.organism_id = sbo.organism_id where ".buildSqlClause(ref_parameters=>\%parameters) . "group by ab.antibody_id,ab.antibody_name,ab.sort_order order by ab.sort_order"; my $stainSql = "select ss.assay_id, assay_name from $TBIS_ASSAY ss join $TBIS_SPECIMEN_BLOCK sb on ss.specimen_block_id = sb.specimen_block_id join $TBIS_SPECIMEN s on sb.specimen_id = s.specimen_id join $TBIS_TISSUE_TYPE tt on s.tissue_type_id = tt.tissue_type_id join $TB_ORGANISM sbo on s.organism_id = sbo.organism_id where ".buildSqlClause(ref_parameters=>\%parameters) . " group by ss.assay_id,ss.assay_name order by ss.assay_name"; my $cellSql = "select ct.structural_unit_id, structural_unit_name from $TBIS_STRUCTURAL_UNIT ct join $TBIS_ASSAY_UNIT_EXPRESSION scp on ct.structural_unit_id = scp.structural_unit_id join $TBIS_ASSAY_CHANNEL ac on scp.assay_channel_id = ac.assay_channel_id join $TBIS_ASSAY ss on ac.assay_id = ss.assay_id join $TBIS_SPECIMEN_BLOCK sb on ss.specimen_block_id = sb.specimen_block_id join $TBIS_SPECIMEN s on sb.specimen_id = s.specimen_id join $TBIS_TISSUE_TYPE tt on s.tissue_type_id = tt.tissue_type_id join $TB_ORGANISM sbo on s.organism_id = sbo.organism_id where ".buildSqlClause(ref_parameters=>\%parameters) . "group by ct.structural_unit_id,ct.structural_unit_name, ct.sort_order order by ct.sort_order"; my $buildClause = buildSqlClause(ref_parameters=>\%parameters); my $antibodyOption; my $stainOption; my $cellOption; #### Process the arguments list my $project_id = $args{'project_id'} || die "project_id not passed"; $antibodyOption = $sbeams->buildOptionList($antibodySql, "Selected","MULTIOPTIONLIST"); my %antibodyOptionHash = $sbeams->selectTwoColumnHash($antibodySql); #collecting all relevant antibody_ids for the user's check my $antibodyString = join ',',keys %antibodyOptionHash; $stainOption = $sbeams->buildOptionList($stainSql, "Selected","MULTIOPTIONLIST"); my %stainOptionHash = $sbeams->selectTwoColumnHash($stainSql); #collecting all revelant stain_ids for the user's check my $stainString = join ',',keys %stainOptionHash; $cellOption = $sbeams->buildOptionList($cellSql, "Selected","MULTIOPTIONLIST"); my %cellOptionHash = $sbeams->selectTwoColumnHash($cellSql); #collecting all relevant cell_type_ids for the user's check my $cellString = join ',', keys %cellOptionHash; #displaying the individual option boxes print $q->start_form; print qq~ Summarized Data keyed on Antibody: ~; print ""; print ""; print ""; print $q->end_form; print $q->start_form; print qq~ Summarized Data keyed on Stains: ~; print ""; print ""; print ""; print $q->end_form; print $q->start_form; print qq~ Summarized Data keyed on CellType: ~; print " "; print ""; print ""; print $q->end_form; #query button is disabled if there are no cell types for this user's query if (!$cellString) { my $func = "disableQuery()"; print "" } #### Finish the table print qq~ ~; return; } sub processAntibody { print "Error, this page is depricated!"; my %args = @_; #### Process the arguments list my $ref_parameters = $args{'ref_parameters'} || die "ref_parameters not passed"; my %parameters = %{$ref_parameters}; my %resultset = (); my $resultset_ref = \%resultset; my %parameters = %{$ref_parameters}; # foreach my $k (keys %parameters) # { # print "$k ==== $parameters{$k}
"; # } #whcih antibodies to display my $includeClause = $parameters{antibody_id}; $includeClause = 'all' if !$includeClause; if ($includeClause eq 'all' ) { $includeClause = $parameters{selection}; } my $limitClause; $limitClause = " and " .$parameters{buildClause} if $parameters{buildClause}; #get some CD information my $sqlCoord = qq~ select antibody_name, alternate_names, biosequence_accession, genome_location+genome_strand, accessor from $TBIS_ANTIBODY ab left join $TBIS_ANTIGEN an on ab.antigen_id = an.antigen_id left join $TBIS_BIOSEQUENCE bs on an.biosequence_id = bs.biosequence_id left join $TBIS_GENOME_COORDINATES gc on bs.biosequence_accession = gc.locus_link_id left join $TBIS_BIOSEQUENCE_SET bss on bs.biosequence_set_id = bss.biosequence_set_id left join $TB_ORGANISM sbo on bss.organism_id = sbo.organism_id left join $TBIS_DBXREF dbx on bs.dbxref_id = dbx.dbxref_id where ab.antibody_id in ($includeClause) and set_Name ='LocusLink' and dbxref_name = 'LocusLink' ~; my @genomeCoord = $sbeams->selectSeveralColumns($sqlCoord); my %genomeHash; foreach my $genome (@genomeCoord) { my %hash; my($name,$alternateName,$locusID,$genomeLocation,$url) = @{$genome}; $hash{alternateName} = $alternateName; $hash{locusLinkID} = $locusID; $hash{locusLinkUrl} = $url."LocRpt.cgi?l=".$locusID; $hash{genomeLocation} = $genomeLocation; $hash{genomeLocationUrl} = 'http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg16&position='.$name; $genomeHash{$name}->{attributes} = \%hash; } my $query = "select ab.antibody_name,ab.antibody_id, ss.assay_name, ss.assay_id, structural_unit_name, ct.structural_unit_id,ct.sort_order, level_name, at_level_percent, si.assay_image_id, si.raw_image_file, si.processed_image_file, si.image_magnification, sbo.organism_name, ISNULL(ac.assay_channel_name, ss.assay_name + ' - chan ' + cast(ac.channel_index as varchar)) as assay_channel_name, ac.assay_channel_id, cpl.level_name from $TBIS_ASSAY ss left join $TBIS_ASSAY_CHANNEL ac on ss.assay_id = ac.assay_id left join $TBIS_ANTIBODY ab on ac.antibody_id = ab.antibody_id left join $TBIS_ASSAY_UNIT_EXPRESSION scp on ac.assay_channel_id = scp.assay_channel_id left join $TBIS_EXPRESSION_LEVEL cpl on scp.expression_level_id = cpl.expression_level_id left join $TBIS_STRUCTURAL_UNIT ct on scp.structural_unit_id = ct.structural_unit_id left join $TBIS_ASSAY_IMAGE si on ac.assay_channel_id = si.assay_channel_id left join $TBIS_SPECIMEN_BLOCK sb on ss.specimen_block_id = sb.specimen_block_id left join $TBIS_SPECIMEN s on sb.specimen_id = s.specimen_id left join $TBIS_TISSUE_TYPE tt on s.tissue_type_id = tt.tissue_type_id left join $TB_ORGANISM sbo on s.organism_id = sbo.organism_id where ab.antibody_id in ( $includeClause ) $limitClause order by ab.sort_order, ct.sort_order"; $sbeams->fetchResultSet(sql_query=>$query,resultset_ref=>$resultset_ref,); my $columHashRef = $resultset_ref->{column_hash_ref}; my $dataArrayRef = $resultset_ref->{data_ref}; my ($count, $prevStainedSlideId,$indexCounter) = 0; my (%stainHash,%cellHash,%stainIdHash,%stainCellHash,%stainLevelHash,%imageIdHash, %imageProcessedHash,%percentHash,%countHash,,%antibodyHash, %cellTypeHash); my ($prevStain,$prevAntibody, %stainChannelHash, %channelHash, %antibodyHash); #arrange the data in a result set we can easily use my $rowCount = scalar(@{$resultset_ref->{data_ref}}); # print "
Back to Main Page <\/A>

Antibody Summary

"; print "

Antibody Summary

Back to Main Page <\/A>"; if ($rowCount < 1) { print "No Data available for this Antibody "; } else { my $antibodyIndex = $resultset_ref->{column_hash_ref}->{antibody_name}; my $antibodyIdIndex = $resultset_ref->{column_hash_ref}->{antibody_id}; my $stainNameIndex = $resultset_ref->{column_hash_ref}->{assay_name}; my $stainedSlideIdIndex = $resultset_ref->{column_hash_ref}->{assay_id}; my $cellNameIndex = $resultset_ref->{column_hash_ref}->{structural_unit_name}; my $cellNameIdIndex = $resultset_ref->{column_hash_ref}->{structural_unit_id}; my $levelIndex = $resultset_ref->{column_hash_ref}->{level_name}; my $levelPercentIndex = $resultset_ref->{column_hash_ref}->{at_level_percent}; my $slideImageIdIndex = $resultset_ref->{column_hash_ref}->{assay_image_id}; my $rawImageFileIndex = $resultset_ref->{column_hash_ref}->{raw_image_file}; my $processedImageFileIndex = $resultset_ref->{column_hash_ref}->{processed_image_file}; my $magnificationIndex = $resultset_ref->{column_hash_ref}->{image_magnification}; #### channel my $channelNameIndex = $resultset_ref->{column_hash_ref}->{assay_channel_name}; my $chanIdIndex = $resultset_ref->{column_hash_ref}->{assay_channel_id}; ####### my $organismNameIndex = $resultset_ref->{column_hash_ref}->{organism_name}; my $stainCount = 0; for (@{$resultset_ref->{data_ref}}) { my @row = @{$resultset_ref->{data_ref}[$indexCounter]}; my $antibody = $row[$antibodyIndex]; my $antibodyNameID = $row[$antibodyIdIndex]; my $stainName = $row[$stainNameIndex]; my $stainedSlideId = $row[$stainedSlideIdIndex]; my $cellType = $row[$cellNameIndex]; my $level = lc($row[$levelIndex]); my $atLevelPercent = $row[$levelPercentIndex]; my $organismName = $row[$organismNameIndex]; my $cellTypeId = $row[$cellNameIdIndex]; ######### channel my $channelName = $row[$channelNameIndex]; my $channelID = $row[$chanIdIndex]; ################# #count number of Stains for an antibody $stainCount++ if $prevStain ne $stainName and $prevAntibody eq $antibody; #get all the images for a Stain my $imageProcessedFlag = 'raw_image_file'; my $imageName = $row[$rawImageFileIndex]; $imageName = $row[$processedImageFileIndex] if $row[$processedImageFileIndex]; $imageProcessedFlag = 'processed_image_file' if $row[$processedImageFileIndex]; ########## channel # $stainHash{$antibody}->{$organismName}->{$stainName}->{$imageName} = $row[$magnificationIndex]; $stainHash{$antibody}->{$organismName}->{$stainName}->{$channelName}->{$imageName} = $row[$magnificationIndex]; $stainChannelHash{$stainName} = $channelName; $channelHash{$channelName} = $channelID; ############ $countHash{$antibody}++ if !$stainIdHash{$stainName}; $stainIdHash{$stainName} = $stainedSlideId; $imageIdHash{$imageName} = $row[$slideImageIdIndex] if $imageName; $imageProcessedHash{$imageName} = $imageProcessedFlag; $antibodyHash{$antibody} = $antibodyNameID; #get all the cell types and the number of the stains available per intensity level per celltype per antibody #this is the number of instances a cell type stains at a certain level $cellHash{$antibody}->{$cellType}->{intense}++ if !$stainCellHash{$stainName}->{$cellType} and $cellType and defined($atLevelPercent); $cellHash{$antibody}->{$cellType}->{equivocal}++ if !$stainCellHash{$stainName}->{$cellType} and $cellType and defined($atLevelPercent); $cellHash{$antibody}->{$cellType}->{none}++ if !$stainCellHash{$stainName}->{$cellType} and $cellType and defined($atLevelPercent); $cellHash{$antibody}->{$cellType}->{count}++if !$stainCellHash{$stainName}->{$cellType} and $cellType; #get the average percent of staining per celltype per level #number of total percent level of intensity (at this level) for a celltype/total number of available stains $percentHash{$antibody}->{$cellType}->{intense} += $atLevelPercent if $row[$levelIndex] eq 'intense' and defined($atLevelPercent) and !$stainLevelHash{$stainName}->{intense}->{$cellType}; $percentHash{$antibody}->{$cellType}->{equivocal} += $atLevelPercent if $row[$levelIndex] eq 'equivocal' and defined($atLevelPercent) and !$stainLevelHash{$stainName}->{equivocal}->{$cellType}; $percentHash{$antibody}->{$cellType}->{none} += $atLevelPercent if $row[$levelIndex] eq 'none' and defined($atLevelPercent) and !$stainLevelHash{$stainName}->{none}->{$cellType}; $cellTypeHash{$cellType} = $row[$cellNameIdIndex]; $antibodyHash{$antibody} = $row[$antibodyIdIndex]; $indexCounter ++; $prevStain = $stainName; $prevAntibody = $antibody; $stainCellHash{$stainName}->{$cellType} = 1; $stainLevelHash{$stainName}->{$level}->{$cellType} = 1; } #have some results for this antibody #count how many experiments, detailed info about staining pattern and print out the stain images %hash_to_sort = %stainHash; #antibody foreach my $antibodyKey (sort bySortOrder keys %stainHash) { my $antibodyID = $antibodyHash{$antibodyKey}; print "

$antibodyKey

"; print ""; print "Alternate names:  $genomeHash{$antibodyKey}->{attributes}->{alternateName}"; print "Locuslink ID:{attributes}->{locusLinkUrl}>   $genomeHash{$antibodyKey}->{attributes}->{locusLinkID}"; print "Genome Coordinates:{attributes}->{genomeLocationUrl}>   $genomeHash{$antibodyKey}->{attributes}->{genomeLocation}"; print "Total Number of Stains: "; print "$countHash{$antibodyKey}"; print "Staining Summmary:"; print qq~ Average PercentageNumber of charaterized Stains Cell Type IntenseEquivocalNone ~if $cellHash{$antibodyKey}; %hash_to_sort = %{$cellHash{$antibodyKey}} if $cellHash{$antibodyKey}; #all about the characterization of the celltypes foreach my $cell (sort bySortOrder keys %{$cellHash{$antibodyKey}}) { my $percentIntense = $percentHash{$antibodyKey}->{$cell}->{'intense'}/$cellHash{$antibodyKey}->{$cell}->{intense} if $cellHash{$antibodyKey}->{$cell}->{intense}; my $percentEquivocal = $percentHash{$antibodyKey}->{$cell}->{'equivocal'}/$cellHash{$antibodyKey}->{$cell}->{equivocal} if $cellHash{$antibodyKey}->{$cell}->{equivocal}; my $percentNone = $percentHash{$antibodyKey}->{$cell}->{'none'}/$cellHash{$antibodyKey}->{$cell}->{none} if $cellHash{$antibodyKey}->{$cell}->{none}; $percentIntense =~ s/^(.*\.\d{3}).*$/$1/; $percentEquivocal =~ s/^(.*\.\d{3}).*$/$1/; $percentNone =~ s/^(.*\.\d{3}).*$/$1/; print "$cell"; print "$percentIntense$percentEquivocal$percentNone"; print "$cellHash{$antibodyKey}->{$cell}->{'count'}"; } #all about the stains foreach my $species (keys %{$stainHash{$antibodyKey}}) { print "$species :"; print qq~ Add a Stain~; #stain foreach my $stain (keys %{$stainHash{$antibodyKey}->{$species}}) { my $stainID = $stainIdHash{$stain}; print "
  • Stain"; print qq~ - $stain~; my ($stainName) = $stain =~ /^.*?\s([\d-]+)/; if ($IMMUNOSPECHASH{$stainName}) { print qq~View Cytometry Data related to this Stain $stainName~; } print "
    • "; #channel if ($stainHash{$antibodyKey}->{$species}->{$stain}) { my $number = scalar (keys(%{$stainHash{$antibodyKey}->{$species}->{$stain}})); $number ++; print "
  • Channel"; print qq~ Add a Channel~; %hash_to_sort = %{$stainHash{$antibodyKey}->{$species}->{$stain}}; my $channelString =''; my $imageString = ''; foreach my $channel (sort bySortOrder keys %{$stainHash{$antibodyKey}->{$species}->{$stain}}) { my $channelId = $channelHash{$channel}; print qq~ - $channel~; print "
    • "; #images if ($stainHash{$antibodyKey}->{$species}->{$stain}->{$channel}) { print "
  • Images"; print qq~ Add an Image~; foreach my $image (sort bySortOrder keys %{$stainHash{$antibodyKey}->{$species}->{$stain}->{$channel}}) { my $magnification = $stainHash{$antibodyKey}->{$species}->{$stain}->{$channel}->{$image}; my $imageID = $imageIdHash{$image}; my $flag = $imageProcessedHash{$image}; $imageString .= " - $magnification x \; \<\/A>" if $imageID; } print "$imageString"; print "
"; } } } } } } print ""; } } sub processStain { my %args = @_; #### Process the arguments list my $ref_parameters = $args{'ref_parameters'} || die "ref_parameters not passed"; my %parameters = %{$ref_parameters}; my %resultset = (); my $resultset_ref = \%resultset; my (%cellHash,%stainHash,%percentHash); =comment foreach my $key (keys %parameters) { print " $key ---- $parameters{$key}
"; } =cut #which stains to display my $includeClause = $parameters{stained_slide_id}; $includeClause = 'all' if !$includeClause; if ($includeClause eq 'all') { $includeClause = $parameters{selection}; } my $query = "Select sbo.organism_name, tt.tissue_type_name, tt.tissue_type_description, sp.surgical_procedure_name, sp.surgical_procedure_description, cd.clinical_diagnosis_name, clinical_diagnosis_description, s.specimen_name, s.specimen_id, sb.specimen_block_name, sb.specimen_block_level,sb.anterior_posterior,sb.specimen_block_side,sb.specimen_block_id, ss.assay_name,ss.assay_id,ss.cancer_amount_cc,ss.preparation_date, si.image_name,si.assay_image_id,si.image_magnification,si.raw_image_file, si.processed_image_file, a.antibody_name, a.antibody_id, an.antigen_name, an.alternate_names, scp.at_level_percent, ct.structural_unit_name,ct.structural_unit_id, cpl.level_name from $TBIS_ASSAY ss left join $TBIS_SPECIMEN_BLOCK sb on ss.specimen_block_id = sb.specimen_block_id left join $TBIS_SPECIMEN s on sb.specimen_id = s.specimen_id left join $TBIS_TISSUE_TYPE tt on s.tissue_type_id = tt.tissue_type_id left join $TBIS_SURGICAL_PROCEDURE sp on s.surgical_procedure_term_id = sp.surgical_procedure_id left join $TBIS_CLINICAL_DIAGNOSIS cd on s.clinical_diagnosis_term_id = cd.clinical_diagnosis_id left join $TBIS_ASSAY_CHANNEL ac on ss.assay_id = ac.assay_id left join $TBIS_ASSAY_IMAGE si on ac.assay_channel_id = si.assay_channel_id left join $TBIS_ANTIBODY a on ac.antibody_id = a.antibody_id left join $TBIS_ASSAY_UNIT_EXPRESSION scp on ac.assay_channel_id = scp.assay_channel_id left join $TBIS_STRUCTURAL_UNIT ct on scp.structural_unit_id = ct.structural_unit_id left join $TBIS_EXPRESSION_LEVEL cpl on scp.expression_level_id = cpl.expression_level_id left join $TBIS_ANTIGEN an on a.antigen_id = an.antigen_id left join $TB_ORGANISM sbo on s.organism_id = sbo.organism_id where ss.assay_id in ($includeClause) order by sbo.sort_order, ct.sort_order,a.sort_order"; my @rows = $sbeams->selectSeveralColumns($query); $log->debug( $query ); print ""; # arrange the data in a result set we can easily use if (scalar(@rows) < 1) { print ""; } else { my (%stainDateHash,%stainOrganismHash,%stainIdHash,%stainAntibodyHash,%antibodyHash,%stainSpecimenHash,%specimenHash,%stainSpecimenBlockHash, %specimenBlockHash,%stainImageHash,%imageHash,%imageFlagHash,%stainCellHash,%stainTissueHash, %stainTissueHash,%antibodyAntigenHash, %organismStainHash,%cellTypeHash); foreach my $row (@rows) { my($organismName,$tissueName,$tissueDesc, $surgicalProc,$surgicalDesc, $clinicalName, $clinicalDesc, $specimenName,$specimenId, $specimenBlock, $specimenLevel,$specimenAP, $specimenSide,$specimenBlockId, $stainName, $stainId, $cancerCC,$prepDate, $imageName,$imageId, $imageMag, $imageRaw, $imageProcessed, $antibody, $antibodyId, $antigen, $antigenAlternate, $levelPercent, $cellType,$cellTypeId, $level) = @{$row}; $prepDate =~ s/^(\d{4}-\d{2}-\d{2}).*$/$1/; $cancerCC =~ s/^(\d?\.\d\d?).*$/$1/; =comment print "a $organismName
b $tissueName
,c $tissueDesc
, d $surgicalProc
,e $surgicalDesc,
f $clinicalName
, g $clinicalDesc
, h $specimenName
i ,$specimenId
, j $specimenBlock
,k $specimenLevel
, l $specimenAP
, m $specimenSide
,n $specimenBlockId
, o $stainName
,p $stainId
, q $cancerCC
r ,$prepDate
, s $imageName
t ,$imageId
,v $imageMag
,w $imageRaw
, x $imageProcessed
, y $antibody
,z $antibodyId
, aa $antigen
,bb $antigenAlternate
, cc $levelPercent
, dd $cellType
, ee $level
"; =cut #all about the oraganism $organismStainHash{$organismName}->{$stainName} = 1; #all about the stain $stainDateHash{$stainName}= $prepDate; $stainOrganismHash{$stainName} = $organismName; $stainIdHash{$stainName} = $stainId; $stainTissueHash{$stainName} = $tissueName; #all about the antibody $stainAntibodyHash{$stainName}->{$antibody}->{$antigen} = $antigenAlternate; $antibodyHash{$antibody} = $antibodyId; $antibodyAntigenHash{$antibody}= $antigen; #all about the specimen unless (! $specimenName) { $surgicalProc =~ s/(\?)/: /; $stainSpecimenHash{$stainName}->{$specimenName}->{$tissueName}->{presence} = 1; $stainSpecimenHash{$stainName}->{$specimenName}->{$tissueName}->{diagnosis} = $clinicalName if $clinicalName; $stainSpecimenHash{$stainName}->{$specimenName}->{$tissueName}->{diagnosisDesc} = $clinicalDesc if $clinicalDesc; $stainSpecimenHash{$stainName}->{$specimenName}->{$tissueName}->{surgical} = $surgicalProc if $surgicalProc; $stainSpecimenHash{$stainName}->{$specimenName}->{$tissueName}->{surgicalDesc} = $surgicalDesc if $surgicalDesc; $stainSpecimenHash{$stainName}->{$specimenName}->{$tissueName}->{tissueDesc} = $tissueDesc if $tissueDesc; $stainSpecimenHash{$stainName}->{$specimenName}->{$tissueName}->{cancerCC} = $cancerCC if $cancerCC; $specimenHash{$specimenName}=$specimenId; $stainTissueHash{$specimenName} = $tissueName; } #all about the specimenBlock if ( $specimenBlock) { $stainSpecimenBlockHash{$stainName}->{$specimenBlock}->{presence} = 1; $specimenAP =~ /a/i?$specimenAP = 'Anterior':$specimenAP='Posterior' if $specimenAP; $specimenSide =~/r/i?$specimenSide='Right':$specimenSide='Left' if($specimenSide); $stainSpecimenBlockHash{$stainName}->{$specimenBlock}->{level} = $specimenLevel if $specimenLevel; $stainSpecimenBlockHash{$stainName}->{$specimenBlock}->{laterality} = $specimenAP if $specimenAP; $stainSpecimenBlockHash{$stainName}->{$specimenBlock}->{side} = $specimenSide if $specimenSide; $specimenBlockHash{$specimenBlock} = $specimenBlockId; } #all about the images unless (! $imageName) { my $imageProcessedFlag = 'raw_image_file'; $imageProcessedFlag = 'processed_image_file' if $imageProcessed; $stainImageHash{$stainName}->{$imageName} = $imageMag; $imageHash{$imageName} = $imageId; $imageFlagHash{$imageName} = $imageProcessedFlag; } if ($cellType) { $level = lc($level); $stainCellHash{$stainName}->{$cellType}->{intense} = $levelPercent if $level eq 'intense'; $stainCellHash{$stainName}->{$cellType}->{equivocal} = $levelPercent if $level eq 'equivocal'; $stainCellHash{$stainName}->{$cellType}->{none} = $levelPercent if $level eq 'none'; $cellTypeHash{$cellType}=$cellTypeId; } } my $what = "Mouse"; my $loopCount = 0; LOOP: %hash_to_sort = %stainSpecimenHash; my $pad = '  '; foreach my $keyStain (sort bySortOrder keys %stainSpecimenHash) { next if $stainOrganismHash{$keyStain} eq $what; print ""; my ($stainName) = $keyStain =~ /^.*?\s([\d-]+)/; if ($IMMUNOSPECHASH{$stainName}) { print qq~~; } print ""; print ""; print ""; print ""; my $antibodyName; %hash_to_sort = %{$stainAntibodyHash{$keyStain}} if $stainAntibodyHash{$keyStain}; foreach my $antibodyKey (sort bySortOrder keys %{$stainAntibodyHash{$keyStain}}) { $antibodyName = $antibodyKey; print qq~ ~; } foreach my $specimenKey (keys %{$stainSpecimenHash{$keyStain}}) { print qq~ ~; foreach my $tissueKey(keys %{$stainSpecimenHash{$keyStain}->{$specimenKey}}) { if ($stainTissueHash{$keyStain} =~ /prostate/i) { my $record = $stainSpecimenHash{$keyStain}->{$specimenKey}->{$tissueKey}; print ""; print ""; print "" unless ($record->{diagnosisDesc}=~/please describe/i or !($record->{diagnosisDesc}));; print ""; print ""; print "" unless ($record->{surgicalDesc} =~/please describe/i or !($record->{surgicalDesc})); print ""; print "" if $record->{cancerCC}; } else { print ""; } } } if ( $stainSpecimenBlockHash{$keyStain}) { if ($stainTissueHash{$keyStain}=~ /prostate/i) { print qq~ ~; print q~ ~ if $stainTissueHash{$keyStain} !~ /bladder/i; print ""; foreach my $specimenBlockKey (keys %{$stainSpecimenBlockHash{$keyStain}}) { print qq~~; print qq~~; } } else { print ""; } } print " END } #this is a hack #as number of stains increased I decided to sort by organism without wanting to change much code $loopCount++; $what = "Human"; goto LOOP if $loopCount ==1; } } sub getTissueHash { my $project_id = shift; my $tissueSql =<<" END"; select s.tissue_type_id,tissue_type_name from $TBIS_SPECIMEN s join $TBIS_TISSUE_TYPE tt on s.tissue_type_id = tt.tissue_type_id WHERE s.project_id = '$project_id' group by tissue_type_name,s.tissue_type_id END return ( $sbeams->selectTwoColumnHash($tissueSql) ); } #when processing the cell type, the user is redirected to SummarizeStains sub processCells { my %args = @_; #### Process the arguments list my $ref_parameters = $args{'ref_parameters'} || die "ref_parameters not passed"; my %parameters = %{$ref_parameters}; my %resultset = (); my $resultset_ref = \%resultset; my $includeClause = $parameters{cell_type_id}; $includeClause = 'all' if !$includeClause; if ($includeClause eq 'all') { $parameters{cell_type_id} = $parameters{selection}; } my $celltypeId = $parameters{cell_type_id}; my $redirectURL = qq~$CGI_BASE_DIR/$SBEAMS_SUBDIR/SummarizeStains?action=QUERY&structural_unit_id=~; my $queryString = "$celltypeId&display_options=MergeLevelsAndPivotCellTypes"; print $q->redirect($redirectURL.$queryString); } #cubersome routine to build the sqlClause #always get the organism_id from sbo since it is the pk(sbeam.dbo.organism) #always get the tissue_type_id from tt since it is the pk(tissue_type) sub buildSqlClause { my %args = @_; #### Process the arguments list my $ref_parameters = $args{'ref_parameters'} || die "ref_parameters not passed"; my %parameters = %{$ref_parameters}; my $project_id = $args{project_id}; my %resultset = (); my $resultset_ref = \%resultset; my $oString = join ',',$parameters{Human},$parameters{Mouse}; $oString =~ s/^\,//; $oString =~ s/\,$//; $oString = qq~ sbo.organism_id in (~.$oString.")" if ($oString); my %tissues = getTissueHash( $project_id ); my $tString = ''; my $sep = ''; for ( keys( %tissues ) ) { $tString .= "$sep $parameters{$_} " if $parameters{$_}; $sep = ',' if $tString; } $tString = qq ~tt.tissue_type_id in (~.$tString .")" if ($tString); my $totalClause; $totalClause = $oString if $oString; $totalClause = $tString if $tString; $totalClause = $oString ." and ". $tString if ($oString and $tString); return $totalClause; } #javascript stuff sub checkGO { my $thashref = shift; my $conditional = ''; my $separator = ''; foreach my $key ( keys( %$thashref ) ) { $conditional .= "$separator(documents.form[3].cbox_${key}.checked)"; $separator = '||' if $conditional; } #making sure an option is checked print q~

Stain Summary

Back to Main Page <\/A>
No Data available for this Stain
 

$keyStain

View Cytometry Data related to this Stain $stainName
Species:$pad $stainOrganismHash{$keyStain}
Tissue Type:$pad $stainTissueHash{$keyStain}
PreparationDate:$pad $stainDateHash{$keyStain}
Antibody:   $antibodyKey
Antigen Alternate Names:   $stainAntibodyHash{$keyStain}->{$antibodyKey}->{$antibodyAntigenHash{$antibodyKey}}
Specimen Name:$pad $specimenKey
Tissue Name:   $tissueKeyTissue Desc:   $record->{tissueDesc}
Clinical Diagnosis:   $record->{diagnosis}Diagnosis Desc   $record->{diagnosisDesc}
Surgical Procedure:   $record->{surgical}Surgical Desc:   $record->{surgicalDesc}
Amount of Cancer:   $record->{cancerCC} cc
SpecimenBlock: NameLevelLaterality Side
   $specimenBlockKey$stainSpecimenBlockHash{$keyStain}->{$specimenBlockKey}->{level} $stainSpecimenBlockHash{$keyStain}->{$specimenBlockKey}->{laterality} $stainSpecimenBlockHash{$keyStain}->{$specimenBlockKey}->{side}
Available Images:"; # if $stainImageHash{$keyStain}; my $line = 1; %hash_to_sort = %{$stainImageHash{$keyStain}} if $stainImageHash{$keyStain}; foreach my $imageKey (sort bySortOrder keys %{$stainImageHash{$keyStain}}) { my $magnification = $stainImageHash{$keyStain}->{$imageKey}; my $flag = $imageFlagHash{$imageKey}; my $imageID = $imageHash{$imageKey}; print qq~~; $line ++; } print "
 $imageKey  $magnification x
None  " if $line == 1; print "
"; # if $stainImageHash{$keyStain}; my $table = SBEAMS::Connection::DataTable->new( BORDER => 1 ); $table->addRow( ['Cell Type', 'Intense', 'Equivocal', 'None' ] ) if $stainCellHash{$keyStain}; %hash_to_sort = %{$stainCellHash{$keyStain}} if $stainCellHash{$keyStain}; foreach my $cellKey (sort bySortOrder keys %{$stainCellHash{$keyStain}}) { my $cellId = $cellTypeHash{$cellKey}; my $antiId = $antibodyHash{$antibodyName}; my $redirectURL = qq~$CGI_BASE_DIR/$SBEAMS_SUBDIR/SummarizeStains?action=QUERY&structural_unit_id=~; my $queryString = "$cellId&antibody_id=$antiId&display_options=MergeLevelsAndPivotCellTypes"; my $record = $stainCellHash{$keyStain}->{$cellKey}; $table->addRow ( [ "$cellKey", $record->{intense}, $record->{equivocal}, $record->{none} ] ); } $table->setColAttr( NOWRAP => 1, COLS => [1..4], ROWS => [1..$table->getRowNum()] ); $table->setColAttr( ALIGN => 'RIGHT', COLS => [2..4], ROWS => [2..$table->getRowNum()] ); print <<" END";
Cell Type Characterization: $table