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soba_multi.cgi
executable file
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soba_multi.cgi
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#!/usr/bin/perl
# partially cleaned up amigo.cgi from 12.204 to only produce SObA 2016 12 14
# /~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&autocompleteValue=F56F4.3%20(Caenorhabditis%20elegans,%20WB:WBGene00018980,%20-,%20-)&showControlsFlag=1
# on wormbase
# root/templates/classes/gene/phenotype_graph.tt2
# lib/WormBase/API/Object/Gene.pm
# root/js/wormbase.js
# anatomy, disease, go, lifestage, and phenotype
# Show "No observed ...", e.g.
# https://wormbase.org/species/c_elegans/gene/WBGene00002159#0b--10
# ZK512.8
# let-4
# WBbt:0006817 0.02
# WBbt:0006814 0.02
# WBbt:0003927 0.02
# WBbt:0006976 0.02
# WBbt:0004096 0.02
# WBbt:0005664 0.02
# WBbt:0003827 0.033
# WBbt:0003826 0.033
# WBbt:0007808 0.033
# WBbt:0007807 0.033
# WBbt:0005668 0.033
# WBbt:0008434 0.033
# WBbt:0008433 0.033
# WBbt:0005661 0.033
# WBbt:0005465 0.036
# WBbt:0005448 0.05
# WBbt:0005835 0.084
# WBbt:0006828 0.087
#
#
# GO:0061458 0.07
# GO:0048569 0.07
# GO:0043632 0.072
# GO:0007568 0.072
# GO:0030163 0.099
use CGI;
use strict;
use HTML::Entities; # for untainting with encode_entities()
use LWP::Simple;
use LWP::UserAgent;
use JSON;
use Tie::IxHash; # allow hashes ordered by item added
use Net::Domain qw(hostname hostfqdn hostdomain);
use URI::Encode qw(uri_encode uri_decode);
use Storable qw(dclone); # copy hash of hashes
use POSIX;
use Time::HiRes qw( time );
my $startTime = time; my $prevTime = time;
$startTime =~ s/(\....).*$/$1/;
$prevTime =~ s/(\....).*$/$1/;
my $hostname = hostname();
my ($cshlHeader, $cshlFooter) = &cshlNew();
# my $top_datatype = 'phenotype';
my $json = JSON->new->allow_nonref;
my $query = new CGI;
# my $base_solr_url = "http://localhost:8080/solr/$top_datatype/"; # big geneontology golr server
my $base_solr_url = "http://localhost:8080/solr/"; # big geneontology golr server
# my $base_solr_url = "http://131.215.12.202:8080/solr/"; # 2020 03 27 - changing this for Raymond
my %paths; # finalpath => array of all (array of nodes of paths that end)
# childToParent -> child node -> parent node => relationship
# # parentToChild -> parent node -> child node => relationship
my %nodesAll; # for an annotated phenotype ID, all nodes in its topological map that have transitivity
my %edgesAll; # for an annotated phenotype ID, all edges in its topological map that have transitivity
my %ancestorNodes;
&process();
sub process {
my $action; # what user clicked
unless ($action = $query->param('action')) { $action = 'none'; }
# http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_biggo.cgi?radio_datatype=phenotype&gene=let-23+%28Caenorhabditis+elegans%2C+WB%3AWBGene00002299%2C+-%2C+ZK1067.1%29&gene=lin-3+%28Caenorhabditis+elegans%2C+WB%3AWBGene00002992%2C+-%2C+F36H1.4%29&action=Graph+Two+Genes
if ($action eq 'annotSummaryCytoscape') { &annotSummaryCytoscape('source_gene'); }
elsif ($action eq 'annotSummaryGraph') { &annotSummaryGraph(); }
elsif ($action eq 'annotSummaryJson') { &annotSummaryJson(); } # temporarily keep this for the live www.wormbase going through the fake phenotype_graph_json widget
elsif ($action eq 'annotSummaryJsonp') { &annotSummaryJsonp(); } # new jsonp widget to get directly from .wormbase without fake widget
elsif ($action eq 'frontPage') { &frontPage(); } # autocomplete on gene names
elsif ($action eq 'Analyze Terms') { &annotSummaryCytoscape('source_ontology'); } # autocomplete on gene names
elsif ($action eq 'autocompleteXHR') { &autocompleteXHR(); }
elsif ($action eq 'autocompleteTazendraXHR') { &autocompleteTazendraXHR(); }
elsif ($action eq 'validateGeneDatatype') { &validateGeneDatatype(); }
elsif ($action eq 'One Gene to SObA Graph') { &pickOneGenePage(); }
elsif ($action eq 'One Gene to Big GO SObA Graph') { &pickOneGeneBiggoPage(); }
elsif ($action eq 'Gene Pair to Big GO SObA Graph') { &pickTwoGenesBiggoPage(); }
elsif ($action eq 'Gene Pair to SObA Graph') { &pickTwoGenesPage(); }
elsif ($action eq 'Terms to SObA Graph') { &pickOntologyTermsPage(); }
elsif ($action eq 'Graph Two Genes') { &annotSummaryCytoscape('source_gene'); }
elsif ($action eq 'Graph One Gene') { &annotSummaryCytoscape('source_gene'); }
else { &frontPage(); } # no action, show dag by default
} # sub process
sub autocompleteXHR {
print "Content-type: text/html\n\n";
my ($var, $words) = &getHtmlVar($query, 'query');
unless ($words) { ($var, $words) = &getHtmlVar($query, 'userValue'); }
($var, my $field) = &getHtmlVar($query, 'field');
if ($field eq 'Gene') { &autocompleteGene($words); }
} # sub autocompleteXHR
sub autocompleteTazendraXHR {
print "Content-type: text/html\n\n";
my ($var, $words) = &getHtmlVar($query, 'query');
($var, my $objectType) = &getHtmlVar($query, 'objectType');
if ($objectType eq 'gene') {
my $url = 'https://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/datatype_objects.cgi?action=autocompleteXHR&objectType=gene&userValue=' . $words;
my $page_data = get $url;
if ($page_data) { print qq($page_data\n); } }
} # sub autocompleteTazendraXHR
sub validateGeneDatatype {
print "Content-type: text/html\n\n";
my ($var, $datatype) = &getHtmlVar($query, 'datatype');
($var, my $gene) = &getHtmlVar($query, 'gene');
my $url = $base_solr_url . $datatype . '/select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=bioentity:%22' . $gene . '%22';
my $page_data = get $url;
my $perl_scalar = $json->decode( $page_data );
my %jsonHash = %$perl_scalar;
if ($jsonHash{'response'}{'numFound'} == 0) { print qq(no data); }
else { print qq(has data); }
} # sub validateGeneDatatype
sub autocompleteGene {
my ($words) = @_;
my ($var, $taxonFq) = &getHtmlVar($query, 'taxonFq');
my ($var, $datatype) = &getHtmlVar($query, 'datatype');
my $max_results = 20;
my $escapedWords = $words;
my $lcwords = lc($escapedWords);
my $ucwords = uc($escapedWords);
$escapedWords =~ s/ /%5C%20/g;
$escapedWords =~ s/:/\\:/g;
my %matches; my $t = tie %matches, "Tie::IxHash"; # sorted hash to filter results
my $datatype_solr_url = $base_solr_url . $datatype . '/';
# Exact match (case sensitive)
my $solr_gene_url = $datatype_solr_url . 'select?qt=standard&fl=score,id,bioentity_internal_id,synonym,bioentity_label,bioentity_name,taxon,taxon_label&version=2.2&wt=json&rows=' . $max_results . '&indent=on&q=*:*&fq=document_category:%22bioentity%22&fq=(bioentity_internal_id:' . $escapedWords . '+OR+bioentity_label:' . $escapedWords . '+OR+bioentity_name:' . $escapedWords . '+OR+synonym:' . $escapedWords . ')';
if ($taxonFq) { $solr_gene_url .= "&fq=($taxonFq)"; }
# print qq($solr_gene_url<br><br>\n\n);
my ($matchesHashref) = &solrSearch( $solr_gene_url, \%matches, $max_results);
%matches = %$matchesHashref;
# String wildcard match (case sensitive)
my $matchesCount = scalar keys %matches;
if ($matchesCount < $max_results) {
my $extraMatchesCount = $max_results - $matchesCount;
$solr_gene_url = $datatype_solr_url . 'select?qt=standard&fl=score,id,bioentity_internal_id,synonym,bioentity_label,bioentity_name,taxon,taxon_label&version=2.2&wt=json&rows=' . $max_results . '&indent=on&q=*:*&fq=document_category:%22bioentity%22&fq=(bioentity_internal_id:' . $escapedWords . '*+OR+bioentity_label:' . $escapedWords . '*+OR+bioentity_name:' . $escapedWords . '*+OR+synonym:' . $escapedWords . '*)';
if ($taxonFq) { $solr_gene_url .= "&fq=($taxonFq)"; }
my ($matchesHashref) = &solrSearch( $solr_gene_url, \%matches, $max_results);
%matches = %$matchesHashref;
}
my @words; my $isPhrase = 0;
if ($words =~ m/[\s\-]/) {
$isPhrase++;
(@words) = split/[\s\-]/, $words; }
if ($isPhrase) {
my $lastWord = pop @words;
my $firstWord = join" ", @words;
my $extraMatchesCount = $max_results - $matchesCount;
$solr_gene_url = $datatype_solr_url . 'select?qt=standard&fl=score,id,bioentity_internal_id,synonym,bioentity_label,bioentity_name,taxon,taxon_label&version=2.2&wt=json&rows=' . $max_results . '&indent=on&q=*:*&fq=document_category:%22bioentity%22&fq=((bioentity_internal_id_searchable:"' . $firstWord . '"+AND+bioentity_internal_id_searchable:' . $lastWord . '*)+OR+(bioentity_name_searchable:"' . $firstWord . '"+AND+bioentity_name_searchable:' . $lastWord . '*)+OR+(bioentity_label_searchable:"' . $firstWord . '"+AND+bioentity_label_searchable:' . $lastWord . '*)+OR+(synonym_searchable:"' . $firstWord . '"+AND+synonym_searchable:' . $lastWord . '*))';
# :8080/solr/$datatype/select?qt=standard&fl=score,id,bioentity_internal_id,bioentity_label,bioentity_name,synonym,taxon,taxon_label&version=2.2&wt=json&rows=500&indent=on&q=*:*&fq=document_category:%22bioentity%22&fq=
if ($taxonFq) { $solr_gene_url .= "&fq=($taxonFq)"; }
my ($matchesHashref) = &solrSearch( $solr_gene_url, \%matches, $max_results);
%matches = %$matchesHashref;
} else { # not a phrase
# Exact match (case insensitive _searchable)
$matchesCount = scalar keys %matches;
if ($matchesCount < $max_results) {
my $extraMatchesCount = $max_results - $matchesCount;
$solr_gene_url = $datatype_solr_url . 'select?qt=standard&fl=score,id,bioentity_internal_id,synonym,bioentity_label,bioentity_name,taxon,taxon_label&version=2.2&wt=json&rows=' . $max_results . '&indent=on&q=*:*&fq=document_category:%22bioentity%22&fq=(bioentity_internal_id_searchable:' . $escapedWords . '+OR+bioentity_label_searchable:' . $escapedWords . '+OR+bioentity_name_searchable:' . $escapedWords . '+OR+synonym_searchable:' . $escapedWords . ')';
if ($taxonFq) { $solr_gene_url .= "&fq=($taxonFq)"; }
my ($matchesHashref) = &solrSearch( $solr_gene_url, \%matches, $max_results);
%matches = %$matchesHashref;
}
# Starting with word Wildcard match (case insensitive _searchable)
$matchesCount = scalar keys %matches;
if ($matchesCount < $max_results) {
my $extraMatchesCount = $max_results - $matchesCount;
$solr_gene_url = $datatype_solr_url . 'select?qt=standard&fl=score,id,bioentity_internal_id,synonym,bioentity_label,bioentity_name,taxon,taxon_label&version=2.2&wt=json&rows=' . $max_results . '&indent=on&q=*:*&fq=document_category:%22bioentity%22&fq=(bioentity_internal_id_searchable:' . $escapedWords . '*+OR+bioentity_label_searchable:' . $escapedWords . '*+OR+bioentity_name_searchable:' . $escapedWords . '*+OR+synonym_searchable:' . $escapedWords . '*)';
if ($taxonFq) { $solr_gene_url .= "&fq=($taxonFq)"; }
my ($matchesHashref) = &solrSearch( $solr_gene_url, \%matches, $max_results);
%matches = %$matchesHashref;
}
}
my $matches = join"\n", keys %matches;
print $matches;
} # sub autocompleteGene
sub validateListTermsQvalue {
my ($data) = @_;
my (@termsQvalue) = split/\n/, $data;
my %types;
my %termsQvalue = ();
my $errorMessage = '';
foreach my $termQvalue (@termsQvalue) {
if ($termQvalue =~ m/\s+$/) { $termQvalue =~ s/\s+$//; }
my ($term, $qvalue) = ('', undef);
my $orig_qvalue = '';
if ($termQvalue =~ m/^(\S+)\s+(.*?)$/) {
($term, $qvalue) = $termQvalue =~ m/^(\S+)\s+(.*?)$/;
if ($qvalue) { $orig_qvalue = $qvalue; }
if ($qvalue == 0) { $qvalue = 1e-100; $orig_qvalue = "zero"; } # for a value of zero
}
elsif ($termQvalue =~ m/^(\S+)\s+$/) {
$term = $1; }
else {
$term = $termQvalue; }
my ($datatype) = &getDatatypeFromObject($term);
$types{$datatype}++;
if ($qvalue == undef) { $qvalue = 0.367879; }
elsif ($qvalue < 1e-100) { $qvalue = 1e-100; }
$termsQvalue{$term}{qvalue} = $qvalue;
$termsQvalue{$term}{orig_qvalue} = $orig_qvalue;
} # foreach my $termQvalue (@termsQvalue)
my @datatypes = keys %types;
my $datatype = join", ", @datatypes;
if ($errorMessage) {
return (0, $errorMessage, \%termsQvalue);
} elsif (scalar @datatypes == 1) {
return (1, $datatype, \%termsQvalue);
} else {
return (0, qq(ERROR invalid datatype "$datatype" found.), \%termsQvalue);
}
} # validateListTermsQvalue
sub getDatatypeFromObject {
my ($focusTermId) = @_;
my ($identifierType) = $focusTermId =~ m/^(\w+):/;
my $lcIdentifierType = lc($identifierType);
my %idToDatatype;
$idToDatatype{"wbbt"} = "anatomy";
$idToDatatype{"doid"} = "disease";
$idToDatatype{"go"} = "go";
$idToDatatype{"wbls"} = "lifestage";
$idToDatatype{"wbphenotype"} = "phenotype";
$idToDatatype{"WBbt"} = "anatomy";
$idToDatatype{"DOID"} = "disease";
$idToDatatype{"GO"} = "go";
$idToDatatype{"WBls"} = "lifestage";
$idToDatatype{"WBPhenotype"} = "phenotype";
if ($idToDatatype{$identifierType}) { return $idToDatatype{$identifierType}; }
elsif ($idToDatatype{$lcIdentifierType}) { return $idToDatatype{$lcIdentifierType}; }
else { return "$focusTermId"; }
} # sub getSolrUrl
sub solrSearch {
my ($solr_gene_url, $matchesHashref, $max_results) = @_;
my $matchesCount = scalar keys %$matchesHashref;
if ($matchesCount < $max_results) {
my $page_data = get $solr_gene_url;
unless ($page_data) { return $matchesHashref; }
my $perl_scalar = $json->decode( $page_data );
my %jsonHash = %$perl_scalar;
foreach my $geneHash (@{ $jsonHash{"response"}{"docs"} }) {
my %geneHash = %$geneHash;
my $id = $geneHash{id} || '-';
my $synonym = '-';
my $synonymRef = $geneHash{synonym} || '';
if ($synonymRef) {
my (@syns) = @$synonymRef;
$synonym = join ", ", @syns; }
my $taxon_label = $geneHash{taxon_label} || '-';
my $bioentity_label = $geneHash{bioentity_label} || '-';
my $bioentity_name = $geneHash{bioentity_name} || '-';
my $entry = qq($bioentity_label ($taxon_label, $id, $bioentity_name, $synonym));
unless ($$matchesHashref{$entry}) { $$matchesHashref{$entry}++; }
}
if (scalar (@{ $jsonHash{"response"}{"docs"} }) >= $max_results) { $$matchesHashref{"more results not shown; narrow your search"}++; }
} # if (scalar keys %matches < $max_results)
return $matchesHashref;
} # sub solrSearch
sub frontPage {
# print "Content-type: text/html\n\n";
# my $header = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><HTML><HEAD>';
# $header .= "<title>$title</title>\n";
# $header .= "</head>";
# $header .= '<body class="yui-skin-sam">';
# print qq($header);
my $title = 'SObA options page';
&printHtmlHeader($title);
print qq(<body class="yui-skin-sam">);
print qq(<form method="get" action="soba_multi.cgi">);
print << "EndOfText";
One Gene to SObA Graph:<br/>
Enter one gene name to obtain a SObA Graph that illustrates annotations.<br/>
<input type="submit" name="action" value="One Gene to SObA Graph"><br/><br/><br/>
Terms to SObA Graph:<br/>
Enter a list of enriched ontology terms (Anatomy, GO or Phenotype, but not mixed), and associated Q (corrected-P) values to obtain a SObA Graph.<br/>
<input type="submit" name="action" value="Terms to SObA Graph"><br/><br/><br/>
Gene Pair to SObA Graph:<br/>
Enter two gene names to obtain a SObA Graph that illustrates their combined annotations.<br/>
<input type="submit" name="action" value="Gene Pair to SObA Graph"><br/><br/><br/>
Big GO One Gene to SObA Graph:<br/>
Enter one gene name to obtain a SObA Graph that illustrates annotations.<br/>
<input type="submit" name="action" value="One Gene to Big GO SObA Graph"><br/><br/><br/>
Big GO Gene Pair to SObA Graph:<br/>
Enter two gene names to obtain a SObA Graph that illustrates their combined annotations.<br/>
<input type="submit" name="action" value="Gene Pair to Big GO SObA Graph"><br/><br/><br/>
EndOfText
print qq(</body></html>);
} # sub frontPage
sub pickOntologyTermsPage {
# print "Content-type: text/html\n\n";
my $title = 'SObA pick a gene';
# my $header = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><HTML><HEAD>';
# $header .= "<title>$title</title>\n";
# print qq($header);
&printHtmlHeader($title);
print qq(<body class="yui-skin-sam">);
# my $exampleData = qq(WBbt:0006817 0.00026\nWBbt:0006814 0.00028\nWBbt:0003927 0.00031\nWBbt:0003737 0.00034\nWBbt:0003721 0.00034\nWBbt:0003740 0.00034\nWBbt:0003724 0.00043\nWBbt:0006762 0.00067\nWBbt:0006764 0.0007\nWBbt:0006763 0.00072\n);
my $exampleData = qq(WBPhenotype:0000012 0.0001\nWBPhenotype:0002056 0.00042\nWBPhenotype:0000462 0.005\nWBPhenotype:0001621 0.049\nWBPhenotype:0000200 0.07\nWBPhenotype:0000033 0.093\n);
print qq(<form method="post" action="soba_multi.cgi">);
print qq(<h3>SObA terms - Enter a list of ontology terms (of the same type) and their associated statistical (correct-P or Q) values for a SObA graph</h3>\n);
print qq(<a href="https://wiki.wormbase.org/index.php/User_Guide/SObA#Pair_of_genes" target="_blank">user guide</a><br/><br/>\n);
print qq(Enter datatype objects paired with q-values on separate lines:<br/>\n);
print qq(<textarea rows="8" cols="80" placeholder="$exampleData" name="objectsQvalue" id="objectsQvalue"></textarea>);
print qq(<input type="hidden" name="filterForLcaFlag" id="filterForLcaFlag" value="1">);
print qq(<input type="hidden" name="filterLongestFlag" id="filterLongestFlag" value="1">);
print qq(<input type="hidden" name="showControlsFlag" id="showControlsFlag" value="0">);
print qq(<input type="submit" name="action" id="analyzePairsButton" value="Analyze Terms"><br/><br/><br/>);
print qq(</form>);
print qq(</body></html>);
} # sub pickOntologyTermsPage
sub pickTwoGenesPage {
# print "Content-type: text/html\n\n";
my $title = 'SObA pick two genes';
&printHtmlHeader($title);
my $header = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><HTML><HEAD>';
$header .= "<style type=\"text/css\">#forcedPersonAutoComplete { width:25em; padding-bottom:2em; } .div-autocomplete { padding-bottom:1.5em; }</style>";
$header .= qq(<style type="text/css">#forcedProcessAutoComplete { width:30em; padding-bottom:2em; } </style>);
$header .= <<"EndOfText";
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/assets/skins/sam/autocomplete.css" />
<link rel="stylesheet" type="text/css" href="https://tazendra.caltech.edu/~azurebrd/stylesheets/jex.css" />
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/fonts/fonts-min.css" />
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/yahoo-dom-event/yahoo-dom-event.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/connection/connection-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/datasource/datasource-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/autocomplete-min.js"></script>
<script type="text/javascript" src="javascript/soba_multi.js"></script>
EndOfText
# $header .= "<title>$title</title>\n";
$header .= "</head>";
$header .= '<body class="yui-skin-sam">';
print qq($header);
print qq(<input type="hidden" name="which_page" id="which_page" value="pickTwoGenesPage">\n);
# my $datatype = 'biggo'; # by defalt for front page
my $datatype = 'phenotype'; # by defalt for front page
my $solr_taxon_url = $base_solr_url . $datatype . '/select?qt=standard&fl=id,taxon,taxon_label&version=2.2&wt=json&rows=0&indent=on&q=*:*&facet=true&facet.field=taxon_label&facet.mincount=1&fq=document_category:%22bioentity%22';
my $page_data = get $solr_taxon_url;
my $perl_scalar = $json->decode( $page_data );
my %jsonHash = %$perl_scalar;
print qq(<form method="get" action="soba_multi.cgi">\n);
print qq(<h3>SObA Gene Pair - combines and compares ontology annotations of a pair of genes</h3>\n);
print qq(<a href="https://wiki.wormbase.org/index.php/User_Guide/SObA#Pair_of_genes" target="_blank">user guide</a><br/><br/>\n);
print qq(Select an ontology to display.<br/>\n);
# UNDO for biggo
# my @datatypes = qw( anatomy disease biggo go lifestage phenotype );
my @datatypes = qw( anatomy disease go lifestage phenotype );
foreach my $datatype (@datatypes) {
my $checked = '';
if ($datatype eq 'phenotype') { $checked = qq(checked="checked"); }
# print qq(<input type="radio" name="radio_datatype" id="radio_datatype" value="$datatype" $checked onclick="setAutocompleteListeners();" >$datatype</input><br/>\n);
print qq(<input type="radio" name="radio_datatype" id="radio_datatype" value="$datatype" $checked onclick="radioDatatypeClick('TwoGenes');" >$datatype</input><br/>\n); }
print qq(<br/>);
my @fieldCount = ('One', 'Two');
my $fieldName = 'geneOneValue';
foreach my $fieldCount (@fieldCount) {
my $countGene = 'first'; if ($fieldCount eq 'Two') { $countGene = 'second'; $fieldName = 'autocompleteValue'; }
print << "EndOfText";
<B>Choose the $countGene gene <!--<span style="color: red;">*</span>--></B>
<font size="-2" color="#3B3B3B">Start typing in a gene and choose from the drop-down.</font>
<span id="messageGene${fieldCount}"></span>
<span id="containerForcedGene${fieldCount}AutoComplete">
<div id="forcedGene${fieldCount}AutoComplete">
<input size="50" name="$fieldName" id="input_Gene${fieldCount}" type="text" style="max-width: 444px; width: 99%; background-color: #E1F1FF;" value="">
<div id="forcedGene${fieldCount}Container"></div>
</div></span><br/><br/>
EndOfText
# UNDO for biggo / species selection
next;
my $div_display = ''; if ($fieldCount eq 'Two') { $div_display = 'style="display: none"'; }
print qq(<div id="controls$fieldCount" $div_display>\n);
print qq(<br/>Prioritize search by selecting one or more species.<br/>\n);
print qq(<select>\n);
my %taxons;
my @priorityTaxons = ( 'Homo sapiens', 'Arabidopsis thaliana', 'Caenorhabditis elegans', 'Danio rerio', 'Drosophila melanogaster', 'Escherichia coli K-12', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae S288c' );
my %priorityTaxons;
foreach my $taxon (@priorityTaxons) {
$priorityTaxons{$taxon}++;
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
# print qq(<input type="checkbox" class="taxon${fieldCount}" name="${fieldCount}$taxon" id="${fieldCount}$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n);
print qq(<option value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</option>\n);
}
# print qq(<br/>);
# print qq(<br/>Additional species.<br/>);
while (scalar (@{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} }) > 0) {
my $taxon = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
my $someNumber = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
next if ($priorityTaxons{$taxon}); # already entered before
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
$taxons{$taxon} = $taxon_plus;
# $taxons{qq(<input type="checkbox" class="taxon${fieldCount}" name="${fieldCount}$taxon" id="${fieldCount}$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n)}++;
}
foreach my $taxon (sort keys %taxons) {
print qq(<option value="$taxons{$taxon}" onclick="setAutocompleteListeners();">$taxon</option>\n);
# print $taxon;
}
print qq(</select>\n);
print qq(</div>\n);
print qq(<br/><br/>\n);
}
print qq(<input type="hidden" name="filterForLcaFlag" value="1">\n);
print qq(<input type="hidden" name="filterLongestFlag" value="1">\n);
print qq(<input type="hidden" name="showControlsFlag" value="0">\n);
print qq(<input type="submit" name="action" value="Graph Two Genes" ></input><br/><br/>\n);
print qq(<input name="reset" type="reset" value="Reset Gene Inputs" onclick="document.getElementById('input_GeneOne').value=''; document.getElementById('input_GeneTwo').value=''; document.getElementById('messageGeneOne').innerHTML =''; document.getElementById('messageGeneTwo').innerHTML ='';"><br/>\n);
print qq(</form>\n);
print qq(</body></html>);
} # sub pickTwoGenesPage
sub pickTwoGenesBiggoPage {
# print "Content-type: text/html\n\n";
my $title = 'SObA pick two genes';
&printHtmlHeader($title);
my $header = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><HTML><HEAD>';
$header .= "<style type=\"text/css\">#forcedPersonAutoComplete { width:25em; padding-bottom:2em; } .div-autocomplete { padding-bottom:1.5em; }</style>";
$header .= qq(<style type="text/css">#forcedProcessAutoComplete { width:30em; padding-bottom:2em; } </style>);
$header .= <<"EndOfText";
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/assets/skins/sam/autocomplete.css" />
<link rel="stylesheet" type="text/css" href="https://tazendra.caltech.edu/~azurebrd/stylesheets/jex.css" />
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/fonts/fonts-min.css" />
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/yahoo-dom-event/yahoo-dom-event.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/connection/connection-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/datasource/datasource-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/autocomplete-min.js"></script>
<script type="text/javascript" src="javascript/soba_multi.js"></script>
EndOfText
$header .= "</head>";
$header .= '<body class="yui-skin-sam">';
print qq($header);
print qq(<input type="hidden" name="which_page" id="which_page" value="pickTwoGenesBiggoPage">\n);
my $datatype = 'biggo'; # by defalt for biggo page
my $solr_taxon_url = $base_solr_url . $datatype . '/select?qt=standard&fl=id,taxon,taxon_label&version=2.2&wt=json&rows=0&indent=on&q=*:*&facet=true&facet.field=taxon_label&facet.mincount=1&fq=document_category:%22bioentity%22';
my $page_data = get $solr_taxon_url;
my $perl_scalar = $json->decode( $page_data );
my %jsonHash = %$perl_scalar;
print qq(<form method="get" action="soba_multi.cgi">\n);
print qq(<h3>SObA Gene Pair - combines and compares ontology annotations of a pair of genes</h3>\n);
print qq(<a href="https://wiki.wormbase.org/index.php/User_Guide/SObA#Pair_of_genes" target="_blank">user guide</a><br/><br/>\n);
print qq(<input type="hidden" name="radio_datatype" id="radio_datatype" value="biggo">\n);
my @fieldCount = ('One', 'Two');
my $fieldName = 'geneOneValue';
my %taxons;
foreach my $fieldCount (@fieldCount) {
my $countGene = 'first'; if ($fieldCount eq 'Two') { $countGene = 'second'; $fieldName = 'autocompleteValue'; }
print << "EndOfText";
<B>Choose the $countGene gene <!--<span style="color: red;">*</span>--></B>
<font size="-2" color="#3B3B3B">Start typing in a gene and choose from the drop-down.</font>
<span id="messageGene${fieldCount}"></span>
<span id="containerForcedGene${fieldCount}AutoComplete">
<div id="forcedGene${fieldCount}AutoComplete">
<input size="50" name="$fieldName" id="input_Gene${fieldCount}" type="text" style="max-width: 444px; width: 99%; background-color: #E1F1FF;" value="">
<div id="forcedGene${fieldCount}Container"></div>
</div></span><br/><br/>
EndOfText
# next to skip / UNDO for biggo / species selection
my $div_display = ''; # if ($fieldCount eq 'Two') { $div_display = 'style="display: none"'; }
print qq(<div id="controls$fieldCount" $div_display>\n);
print qq(<br/>Prioritize search by selecting a species.<br/>\n);
print qq(<select id="taxon${fieldCount}">\n);
print qq(<option value="All" onclick="setAutocompleteListeners();">All</option>\n);
my @priorityTaxons = ( 'Homo sapiens', 'Arabidopsis thaliana', 'Caenorhabditis elegans', 'Danio rerio', 'Drosophila melanogaster', 'Escherichia coli K-12', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae S288c' );
my %priorityTaxons;
foreach my $taxon (@priorityTaxons) {
$priorityTaxons{$taxon}++;
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
print qq(<option value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</option>\n);
# to use checkboxes instead of dropdown
# print qq(<input type="checkbox" class="taxon${fieldCount}" name="${fieldCount}$taxon" id="${fieldCount}$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n);
}
print qq(<br/>);
print qq(<br/>Additional species.<br/>);
while (scalar (@{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} }) > 0) {
my $taxon = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
my $someNumber = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
next if ($priorityTaxons{$taxon}); # already entered before
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
$taxons{$taxon} = $taxon_plus;
# to use checkboxes instead of dropdown
# $taxons{qq(<input type="checkbox" class="taxon${fieldCount}" name="${fieldCount}$taxon" id="${fieldCount}$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n)}++;
}
foreach my $taxon (sort keys %taxons) {
print qq(<option value="$taxons{$taxon}" onclick="setAutocompleteListeners();">$taxon</option>\n);
# to use checkboxes instead of dropdown
# print $taxon;
}
print qq(</select>\n);
print qq(</div>\n);
print qq(<br/><br/>\n);
}
print qq(<input type="hidden" name="filterForLcaFlag" value="1">\n);
print qq(<input type="hidden" name="filterLongestFlag" value="1">\n);
print qq(<input type="hidden" name="showControlsFlag" value="0">\n);
print qq(<input type="submit" name="action" value="Graph Two Genes" ></input><br/><br/>\n);
print qq(<input name="reset" type="reset" value="Reset Gene Inputs" onclick="document.getElementById('input_GeneOne').value=''; document.getElementById('input_GeneTwo').value=''; document.getElementById('messageGeneOne').innerHTML =''; document.getElementById('messageGeneTwo').innerHTML ='';"><br/>\n);
print qq(</form>\n);
print qq(</body></html>);
} # sub pickTwoGenesBiggoPage
sub pickOneGeneBiggoPage {
# print "Content-type: text/html\n\n";
my $title = 'SObA pick a Big GO gene';
&printHtmlHeader($title);
my $header = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><HTML><HEAD>';
$header .= "<title>$title</title>\n";
$header .= "<style type=\"text/css\">#forcedPersonAutoComplete { width:25em; padding-bottom:2em; } .div-autocomplete { padding-bottom:1.5em; }</style>";
$header .= qq(<style type="text/css">#forcedProcessAutoComplete { width:30em; padding-bottom:2em; } </style>);
$header .= <<"EndOfText";
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/assets/skins/sam/autocomplete.css" />
<link rel="stylesheet" type="text/css" href="https://tazendra.caltech.edu/~azurebrd/stylesheets/jex.css" />
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/fonts/fonts-min.css" />
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/yahoo-dom-event/yahoo-dom-event.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/connection/connection-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/datasource/datasource-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/autocomplete-min.js"></script>
<script type="text/javascript" src="javascript/soba_multi.js"></script>
EndOfText
$header .= "</head>";
$header .= '<body class="yui-skin-sam">';
print qq($header);
print qq(<input type="hidden" name="which_page" id="which_page" value="pickOneGeneBiggoPage">\n);
my $datatype = 'biggo'; # by defalt for front page
# my $datatype = 'phenotype'; # by defalt for front page
my $solr_taxon_url = $base_solr_url . $datatype . '/select?qt=standard&fl=id,taxon,taxon_label&version=2.2&wt=json&rows=0&indent=on&q=*:*&facet=true&facet.field=taxon_label&facet.mincount=1&fq=document_category:%22bioentity%22';
my $page_data = get $solr_taxon_url;
my $perl_scalar = $json->decode( $page_data );
my %jsonHash = %$perl_scalar;
print qq(<form method="get" action="soba_multi.cgi">\n);
print qq(<input type="hidden" name="radio_datatype" id="radio_datatype" value="biggo"\n);
print << "EndOfText";
<B>Choose a gene <!--<span style="color: red;">*</span>--></B>
<font size="-2" color="#3B3B3B">Start typing in a gene and choose from the drop-down.</font>
<span id="containerForcedGeneAutoComplete">
<div id="forcedGeneAutoComplete">
<input size="50" name="autocompleteValue" id="input_Gene" type="text" style="max-width: 444px; width: 99%; background-color: #E1F1FF;" value="">
<div id="forcedGeneContainer"></div>
</div></span><br/><br/>
EndOfText
print qq(Prioritize search by selecting a species.<br/>\n);
my %taxons;
print qq(<select id="taxon_all">\n);
print qq(<option value="All" onclick="setAutocompleteListeners();">All</option>\n);
# print qq(<input type="checkbox" class="taxon_all" name="taxon_all" id="taxon_all" value="all" checked="checked">All Taxons</input><br/>\n);
my @priorityTaxons = ( 'Homo sapiens', 'Arabidopsis thaliana', 'Caenorhabditis elegans', 'Danio rerio', 'Drosophila melanogaster', 'Escherichia coli K-12', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae S288c' );
my %priorityTaxons;
foreach my $taxon (@priorityTaxons) {
$priorityTaxons{$taxon}++;
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
print qq(<option value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</option>\n);
# to use checkboxes instead of dropdown
# print qq(<input type="checkbox" class="taxon" name="$taxon" id="$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n);
}
print qq(<br/>);
print qq(<br/>Additional species.<br/>);
while (scalar (@{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} }) > 0) {
my $taxon = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
my $someNumber = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
next if ($priorityTaxons{$taxon}); # already entered before
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
$taxons{$taxon} = $taxon_plus;
# to use checkboxes instead of dropdown
# $taxons{qq(<input type="checkbox" class="taxon" name="$taxon" id="$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n)}++;
}
foreach my $taxon (sort keys %taxons) {
print qq(<option value="$taxons{$taxon}" onclick="setAutocompleteListeners();">$taxon</option>\n);
# to use checkboxes instead of dropdown
print $taxon;
}
print qq(</select><br/><br/>\n);
print qq(<input type="hidden" name="filterForLcaFlag" value="1">\n);
print qq(<input type="hidden" name="filterLongestFlag" value="1">\n);
print qq(<input type="hidden" name="showControlsFlag" value="0">\n);
print qq(<input type="submit" name="action" value="Graph One Gene"><br/><br/>\n);
print qq(<input name="reset" type="reset" value="Reset Gene Input" onclick="document.getElementById('input_Gene').value='';"><br/>\n);
print qq(</form>\n);
print qq(</body></html>);
} # sub pickOneGeneBiggoPage
sub pickOneGenePage {
# print "Content-type: text/html\n\n";
my $title = 'SObA pick a gene';
&printHtmlHeader($title);
my $header = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><HTML><HEAD>';
$header .= "<title>$title</title>\n";
# $header .= '<link rel="stylesheet" href="https://tazendra.caltech.edu/~azurebrd/stylesheets/jex.css" />';
# $header .= "<link rel=\"stylesheet\" type=\"text/css\" href=\"http://yui.yahooapis.com/2.7.0/build/autocomplete/assets/skins/sam/autocomplete.css\" />";
$header .= "<style type=\"text/css\">#forcedPersonAutoComplete { width:25em; padding-bottom:2em; } .div-autocomplete { padding-bottom:1.5em; }</style>";
$header .= qq(<style type="text/css">#forcedProcessAutoComplete { width:30em; padding-bottom:2em; } </style>);
# <link rel="stylesheet" type="text/css" href="../yui/2.7.0/build/autocomplete/assets/skins/sam/autocomplete.css" />
# <link rel="stylesheet" type="text/css" href="../stylesheets/jex.css" />
# <link rel="stylesheet" type="text/css" href="../yui/2.7.0/build/fonts/fonts-min.css" />
# <script type="text/javascript" src="../yui/2.7.0/build/yahoo-dom-event/yahoo-dom-event.js"></script>
# <script type="text/javascript" src="../yui/2.7.0/build/connection/connection-min.js"></script>
# <script type="text/javascript" src="../yui/2.7.0/build/datasource/datasource-min.js"></script>
# <script type="text/javascript" src="../yui/2.7.0/build/autocomplete/autocomplete-min.js"></script>
# <script type="text/javascript" src="../javascript/soba_multi.js"></script>
$header .= <<"EndOfText";
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/assets/skins/sam/autocomplete.css" />
<link rel="stylesheet" type="text/css" href="https://tazendra.caltech.edu/~azurebrd/stylesheets/jex.css" />
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/fonts/fonts-min.css" />
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/yahoo-dom-event/yahoo-dom-event.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/connection/connection-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/datasource/datasource-min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/yui/2.7.0/autocomplete/autocomplete-min.js"></script>
<script type="text/javascript" src="javascript/soba_multi.js"></script>
EndOfText
$header .= "</head>";
$header .= '<body class="yui-skin-sam">';
print qq($header);
print qq(<input type="hidden" name="which_page" id="which_page" value="pickOneGenePage">\n);
# my $datatype = 'biggo'; # by defalt for front page
my $datatype = 'phenotype'; # by defalt for front page
my $solr_taxon_url = $base_solr_url . $datatype . '/select?qt=standard&fl=id,taxon,taxon_label&version=2.2&wt=json&rows=0&indent=on&q=*:*&facet=true&facet.field=taxon_label&facet.mincount=1&fq=document_category:%22bioentity%22';
my $page_data = get $solr_taxon_url;
my $perl_scalar = $json->decode( $page_data );
my %jsonHash = %$perl_scalar;
print qq(<form method="get" action="soba_multi.cgi">\n);
print qq(Select a datatype to display.<br/>\n);
# UNDO for biggo
# my @datatypes = qw( anatomy disease biggo go lifestage phenotype );
my @datatypes = qw( anatomy disease go lifestage phenotype );
foreach my $datatype (@datatypes) {
my $checked = '';
if ($datatype eq 'phenotype') { $checked = qq(checked="checked"); }
print qq(<input type="radio" name="radio_datatype" id="radio_datatype" value="$datatype" $checked onclick="setAutocompleteListeners();" >$datatype</input><br/>\n); }
print qq(<br/>);
print << "EndOfText";
<B>Choose a gene <!--<span style="color: red;">*</span>--></B>
<font size="-2" color="#3B3B3B">Start typing in a gene and choose from the drop-down.</font>
<span id="containerForcedGeneAutoComplete">
<div id="forcedGeneAutoComplete">
<input size="50" name="autocompleteValue" id="input_Gene" type="text" style="max-width: 444px; width: 99%; background-color: #E1F1FF;" value="">
<div id="forcedGeneContainer"></div>
</div></span><br/><br/>
EndOfText
print qq(<input type="hidden" name="filterForLcaFlag" value="1">\n);
print qq(<input type="hidden" name="filterLongestFlag" value="1">\n);
print qq(<input type="hidden" name="showControlsFlag" value="0">\n);
print qq(<input type="submit" name="action" value="Graph One Gene"><br/><br/>\n);
print qq(<input name="reset" type="reset" value="Reset Gene Input" onclick="document.getElementById('input_Gene').value='';"><br/>\n);
print qq(<div style="display:none">);
print qq(<br/>Prioritize search by selecting one or more species.<br/>\n);
my %taxons;
# print qq(<input type="checkbox" class="taxon_all" name="taxon_all" id="taxon_all" value="all" checked="checked">All Taxons</input><br/>\n);
my @priorityTaxons = ( 'Homo sapiens', 'Arabidopsis thaliana', 'Caenorhabditis elegans', 'Danio rerio', 'Drosophila melanogaster', 'Escherichia coli K-12', 'Mus musculus', 'Rattus norvegicus', 'Saccharomyces cerevisiae S288c' );
my %priorityTaxons;
foreach my $taxon (@priorityTaxons) {
$priorityTaxons{$taxon}++;
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
print qq(<input type="checkbox" class="taxon" name="$taxon" id="$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n);
}
print qq(<br/>);
print qq(<br/>Additional species.<br/>);
while (scalar (@{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} }) > 0) {
my $taxon = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
my $someNumber = shift @{ $jsonHash{"facet_counts"}{"facet_fields"}{"taxon_label"} };
next if ($priorityTaxons{$taxon}); # already entered before
my $taxon_plus = $taxon; $taxon_plus =~ s/ /+/g;
$taxons{qq(<input type="checkbox" class="taxon" name="$taxon" id="$taxon" value="$taxon_plus" onclick="setAutocompleteListeners();">$taxon</input><br/>\n)}++;
}
foreach my $taxon (sort keys %taxons) {
print $taxon;
}
print qq(</div>);
print qq(</form>\n);
print qq(</body></html>);
} # sub pickOneGenePage
sub calcNodeWidth {
my ($nodeCount, $maxAnyCount) = @_;
unless ($nodeCount) { $nodeCount = 1; } # some values generated from enrichment don't have a count, default to smallest
unless ($maxAnyCount) { $maxAnyCount = 1; }
my $nodeWidth = 1; my $nodeScale = 1.5; my $nodeMinSize = 0.01;
# my $logScaler = .6;
$nodeWidth = ( sqrt($nodeCount)/sqrt($maxAnyCount) * $nodeScale ) + $nodeMinSize;
# print qq(NC $nodeCount MAC $maxAnyCount NW $nodeWidth E\n);
return $nodeWidth;
} # sub calcNodeWidth
sub getDiffTime {
my ($start, $prev, $message) = @_;
my $now = time;
$now =~ s/(\....).*$/$1/;
my $diffStart = $now - $startTime;
$diffStart =~ s/(\....).*$/$1/;
my $diffPrev = $now - $prevTime;
$diffPrev =~ s/(\....).*$/$1/;
$prevTime = $now;
$message = qq($diffStart seconds from start, $diffPrev seconds from previous check. Now $message);
return ($message);
} # sub getDiffTime
sub calculateNodesAndEdges {
my ($focusTermId, $geneOneId, $objectsQvalue, $datatype, $rootsChosen, $filterForLcaFlag, $maxDepth, $maxNodes) = @_;
my (@parentNodes) = split/,/, $rootsChosen;
unless ($datatype) { $datatype = 'phenotype'; } # later will need to change based on different datatypes
# if ($datatype eq 'phenotype') { # FIX should come from function call
# @parentNodes = ( 'WBPhenotype:0000886'); # TESTING , doesn't work 2019 03 01
# }
# # radio_etgo=radio_etgo_withiea&rootsChosen=&maxNodes=0&maxDepth=0&filterLongestFlag=0&filterForLcaFlag=1
# # radio_etgo=radio_etgo_withiea&rootsChosen= &showControlsFlag=1&fakeRootFlag=0&filterForLcaFlag=1&filterLongestFlag=0&maxNodes=0&maxDepth=0
# # radio_etgo= &rootsChosen=WBPhenotype:0000886&showControlsFlag=1 &filterForLcaFlag=0&filterLongestFlag=0&maxNodes=0&maxDepth=0
my ($var, $radio_etgo) = &getHtmlVar($query, 'radio_etgo');
my ($var, $radio_etp) = &getHtmlVar($query, 'radio_etp');
my ($var, $radio_etd) = &getHtmlVar($query, 'radio_etd');
my ($var, $radio_eta) = &getHtmlVar($query, 'radio_eta');
my $toReturn = '';
my $solr_url = $base_solr_url . $datatype . '/';
# link 1, from wbgene get wbphenotypes from "grouped":{ "annotation_class":{ "matches":12, "ngroups":4, "groups":[{ "groupValue":"WBPhenotype:0000674", # }]}}
my %allLca; # all nodes that are LCA to any pair of annotated terms
my %nodes; # node -> 'counts' -> $whichGene/'anygene' -> $evidenceType/'anytype'
# node -> qvalue
# node -> orig_qvalue
# node -> label
# node -> annot annotated node
# node -> lca lca node
my %edgesPtc; # edges from parent to child
my $nodeWidth = 1;
my $weightedNodeWidth = 1;
my $unweightedNodeWidth = 1;
my %annotationNodeidWhichgene = (); # annotation state 'annot' vs 'any' -> nodeid -> which gene 'geneOne' or 'geneTwo'
my @annotNodeIds; # array of annotated terms to loop and do pairwise comparisons
my %termsQvalue; # map term to qvalue from user input
# START
my @geneIds = ();
if ($focusTermId) {
push @geneIds, $focusTermId;
if ($geneOneId) { push @geneIds, $geneOneId; }
foreach my $geneId (@geneIds) {
my $whichGene = 'geneOne';
if ($geneId eq $focusTermId) { $whichGene = 'geneTwo'; }
# print qq(FT $focusTermId E\n);
my $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=bioentity:%22' . $geneId . '%22';
if ($radio_etgo) {
if ($radio_etgo eq 'radio_etgo_excludeiea') { $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=-evidence_type:IEA&fq=bioentity:%22' . $geneId . '%22'; }
elsif ($radio_etgo eq 'radio_etgo_onlyiea') { $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=bioentity,regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=evidence_type:(EXP+IDA+IPI+IMP+IGI+IEP)&fq=bioentity:%22' . $geneId . '%22'; } }
if ($radio_etp) {
if ($radio_etp eq 'radio_etp_onlyvariation') { $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=evidence_type:Variation&fq=bioentity:%22' . $geneId . '%22'; }
elsif ($radio_etp eq 'radio_etp_onlyrnai') { $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=evidence_type:RNAi&fq=bioentity:%22' . $geneId . '%22'; } }
if ($radio_etd) {
if ($radio_etd eq 'radio_etd_excludeiea') { $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=-evidence_type:IEA&fq=bioentity:%22' . $geneId . '%22'; } }
if ($radio_eta) {
if ($radio_eta eq 'radio_eta_onlyexprcluster') { $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=id:(*WB\:WBPaper*)&fq=bioentity:%22' . $geneId . '%22'; }
elsif ($radio_eta eq 'radio_eta_onlyexprpattern') { $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=id:(*WB\:Expr*+*WB\:Marker*)&fq=bioentity:%22' . $geneId . '%22'; } }
# Anatomy, Expr and Expression_cluster (ref.
# https://wormbase.org/tools/ontology_browser/show_genes?focusTermName=Anatomy&focusTermId=WBbt:0005766).
# There are three groups of objects WB:Expr***, WBMarker*** (these are Expression patterns), WB:WBPaper*** (these are Expression profiles).
# amigo.cgi query
# $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=bioentity:%22WB:' . $geneId . '%22';
my $page_data = get $annotation_count_solr_url; # get the URL
# print qq( annotation_count_solr_url $annotation_count_solr_url\n); # get the URL
# numFound == 0
my $perl_scalar = $json->decode( $page_data ); # get the solr data
my %jsonHash = %$perl_scalar;
# if ($jsonHash{'response'}{'numFound'} == 0) { return ($toReturn, \%nodes, \%nodes); } # return nothing if there are no annotations found
next if ($jsonHash{'response'}{'numFound'} == 0); # skip if there are no annotations found, can't return because could have 2 genes
foreach my $doc (@{ $jsonHash{'response'}{'docs'} }) {
my $nodeIdAnnotated = $$doc{'annotation_class'};
$annotationNodeidWhichgene{'annot'}{$nodeIdAnnotated}{$whichGene}++;
$annotationNodeidWhichgene{'any'}{$nodeIdAnnotated}{$whichGene}++;
my $id = $$doc{'id'};
my (@idarray) = split/\t/, $id;
if ($datatype eq 'anatomy') {
my @entries = split/\|/, $idarray[7];
foreach my $entry (@entries) {
my $evidenceType = '';
if ($entry =~ m/^WB:Expr/) { $evidenceType = 'Expression Pattern'; }
elsif ($entry =~ m/^WBMarker/) { $evidenceType = 'Expression Pattern'; }
elsif ($entry =~ m/^WB:WBPaper/) { $evidenceType = 'Expression Cluster'; }
if ($evidenceType) {
# FIX ? nodeIdInferred -> nodeIdAnnotany ?
foreach my $nodeIdInferred (@{ $$doc{'regulates_closure'} }) {
# print qq(NODE whichGene $whichGene GOID $nodeIdInferred 1\n);
$annotationNodeidWhichgene{'any'}{$nodeIdInferred}{$whichGene}++; # track which gene inferred nodes came from
# $nodes{$nodeIdInferred}{'counts'}{'any'}++; $nodes{$nodeIdInferred}{'counts'}{$evidenceType}++;
$nodes{$nodeIdInferred}{'counts'}{'anygene'}{'anytype'}++; $nodes{$nodeIdInferred}{'counts'}{'anygene'}{$evidenceType}++;
$nodes{$nodeIdInferred}{'counts'}{$whichGene}{'anytype'}++; $nodes{$nodeIdInferred}{'counts'}{$whichGene}{$evidenceType}++; } } } }
else {
my $evidenceType = $idarray[6];
if ($datatype eq 'lifestage') { if ($evidenceType eq 'IDA') { $evidenceType = 'Gene Expression'; } }
foreach my $nodeIdInferred (@{ $$doc{'regulates_closure'} }) {
# print qq(NODE whichGene $whichGene GOID $nodeIdInferred 2\n);
$annotationNodeidWhichgene{'any'}{$nodeIdInferred}{$whichGene}++; # track which gene inferred nodes came from
# $nodes{$nodeIdInferred}{'counts'}{'any'}++; $nodes{$nodeIdInferred}{'counts'}{$evidenceType}++;
$nodes{$nodeIdInferred}{'counts'}{'anygene'}{'anytype'}++; $nodes{$nodeIdInferred}{'counts'}{'anygene'}{$evidenceType}++;
$nodes{$nodeIdInferred}{'counts'}{$whichGene}{'anytype'}++; $nodes{$nodeIdInferred}{'counts'}{$whichGene}{$evidenceType}++; } }
} # foreach my $doc (@{ $jsonHash{'response'}{'docs'} })
} # foreach my $geneId (@geneIds)
} # if ($focusTermId)
elsif ($objectsQvalue) {
my ($is_ok, $termsQvalue_datatype, $termsQvalueHref) = &validateListTermsQvalue($objectsQvalue);
if ($is_ok) {
my $whichGene = 'geneOne';
%termsQvalue = %$termsQvalueHref;
foreach my $term (sort keys %termsQvalue) {
my $qvalue = $termsQvalue{$term}{qvalue};
my $orig_qvalue = $termsQvalue{$term}{orig_qvalue};
$qvalue = $qvalue + 0; # for some reason this has a linebreak after it, needs to be a number for json
if ($qvalue == 0) { $qvalue = 0.1; }
my $scaling = 0;
# $scaling = 1 / $qvalue;
# $scaling = -1 * log($qvalue);
if ($qvalue) {
$scaling = -1 * log($qvalue); }
$nodes{$term}{'counts'}{'anygene'}{'anytype'} = $scaling;
$nodes{$term}{'qvalue'} = $qvalue;
$nodes{$term}{'orig_qvalue'} = $orig_qvalue;
# print qq(TERM $term V $termsQvalue{$term}{qvalue} S $scaling E\n);
$annotationNodeidWhichgene{'annot'}{$term}{$whichGene}++;
$annotationNodeidWhichgene{'any'}{$term}{$whichGene}++;
} # foreach my $term (sort keys %termsQvalue)
}
else { print qq(Terms did not validate properly. $termsQvalue_datatype<br>\n); }
}
# END
# amigo.cgi
# my $annotation_count_solr_url = $solr_url . 'select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=bioentity:%22WB:' . $focusTermId . '%22';
# my $phenotype_solr_url = $solr_url . 'select?qt=standard&fl=regulates_transitivity_graph_json,topology_graph_json&version=2.2&wt=json&indent=on&rows=1&fq=-is_obsolete:true&fq=document_category:%22ontology_class%22&q=id:%22' . $phenotypeId . '%22';
my $errorMessage = '';
foreach my $nodeIdAnnotated (sort keys %{ $annotationNodeidWhichgene{'annot'} }) {
push @annotNodeIds, $nodeIdAnnotated;
my $phenotype_solr_url = $solr_url . 'select?qt=standard&fl=regulates_transitivity_graph_json,topology_graph_json&version=2.2&wt=json&indent=on&rows=1&fq=-is_obsolete:true&fq=document_category:%22ontology_class%22&q=id:%22' . $nodeIdAnnotated . '%22';
my $page_data = get $phenotype_solr_url; # get the URL
# print qq( phenotype_solr_url $phenotype_solr_url\n);
my $perl_scalar = $json->decode( $page_data ); # get the solr data
my %jsonHash = %$perl_scalar;
if ($jsonHash{'response'}{'numFound'} == 0) { $errorMessage .= qq($nodeIdAnnotated not found<br/>); }
next unless ($jsonHash{"response"}{"docs"}[0]{"regulates_transitivity_graph_json"} ); # term must have data to extra json from it
my $transHashref = $json->decode( $jsonHash{"response"}{"docs"}[0]{"regulates_transitivity_graph_json"} );
my %transHash = %$transHashref;
my (@nodes) = @{ $transHash{"nodes"} };
my %transNodes; # track transitivity nodes as nodes to keep from topology data
for my $index (0 .. @nodes) { if ($nodes[$index]{'id'}) { my $id = $nodes[$index]{'id'}; $transNodes{$id}++; } }
my $topoHashref = $json->decode( $jsonHash{"response"}{"docs"}[0]{"topology_graph_json"} );
my %topoHash = %$topoHashref;
my (@edges) = @{ $topoHash{"edges"} };
for my $index (0 .. @edges) { # for each edge, add to graph
my ($sub, $obj, $pred) = ('', '', ''); # subject object predicate from topology_graph_json
if ($edges[$index]{'sub'}) { $sub = $edges[$index]{'sub'}; }
if ($edges[$index]{'obj'}) { $obj = $edges[$index]{'obj'}; }
next unless ( ($transNodes{$sub}) && ($transNodes{$obj}) );
if ($edges[$index]{'pred'}) { $pred = $edges[$index]{'pred'}; }
# my $direction = 'back'; my $style = 'solid'; # graph arror direction and style
if ($sub && $obj && $pred) { # if subject + object + predicate
$edgesAll{$nodeIdAnnotated}{$sub}{$obj}++; # for an annotated term's edges, each child to its parents
$edgesPtc{$obj}{$sub}++; # any existing edge, parent to child
} # if ($sub && $obj && $pred)
} # for my $index (0 .. @edges)
my (@nodes) = @{ $topoHash{"nodes"} };
for my $index (0 .. @nodes) { # for each node, add to graph
my ($id, $lbl) = ('', ''); # id and label
if ($nodes[$index]{'id'}) { $id = $nodes[$index]{'id'}; }
if ($nodes[$index]{'lbl'}) { $lbl = $nodes[$index]{'lbl'}; }
next unless ($id);
# UNDO THIS
# $lbl = "$id - $lbl"; # for debugging to find IDs in graph
$nodes{$id}{label} = $lbl;
next unless ($transNodes{$id}); # skip adding node if it's not in transitivity (otherwise, e.g. biggo WBGene00002992 gets GO:0031224 is LCA of GO:0016020 and GO:0016021)
# # $lbl =~ s/ /<br\/>/g; # replace spaces with html linebreaks in graph for more-square boxes
# my $label = "$lbl"; # node label should have full id, not stripped of :, which is required for edge title text
# if ($nodes{$id}) { # if there are annotation counts to variation and/or rnai, add them to the box
# my $annotCounts = '';
# foreach my $whichGene (sort keys %{ $nodes{$id}{'counts'} }) {
# next if ($whichGene eq 'anygene'); # skip 'anygene', only use geneOne / geneTwo
# $annotCounts .= $whichGene . ' - ';
# my @annotCounts;
# foreach my $evidenceType (sort keys %{ $nodes{$id}{'counts'}{$whichGene} }) {
# next if ($evidenceType eq 'anytype'); # skip 'anytype', only used for relative size to max value
# push @annotCounts, qq($nodes{$id}{'counts'}{$whichGene}{$evidenceType} $evidenceType); }
# $annotCounts .= join"; ", @annotCounts; }
# $annotCounts .= "\n";
# $label = qq(LINEBREAK<br\/>$label<br\/><font color="transparent">$annotCounts<\/font>); # add html line break and annotation counts to the label
# }
# print qq(ID $id LBL $lbl E\n);
if ($id && $lbl) {
# if ( ($nodeIdAnnotated eq 'GO:0016021') || ($nodeIdAnnotated eq 'GO:0016020') ) { print qq(ADDING $nodeIdAnnotated TO $id LBL $lbl\n); }
$nodesAll{$nodeIdAnnotated}{$id} = $lbl;
# print qq(nodesAll $nodeIdAnnotated ID $id LBL $lbl E\n);
}
}
} # foreach my $nodeIdAnnotated (sort keys %{ $annotationNodeidWhichgene{'annot'} })