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Copy pathTextpressoDisplayTasks.pm
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TextpressoDisplayTasks.pm
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package TextpressoDisplayTasks;
# Package provide class and methods for
# tasks related to displaying and maintaining
# Webpages
#
# (c) 2007 Hans-Michael Muller, Caltech, Pasadena,
# with contributions by Arun Rangarajan.
use strict;
use POSIX;
use TextpressoGeneralGlobals;
use TextpressoDisplayGlobals;
use TextpressoDatabaseGlobals;
use TextpressoDatabaseCategories;
use TextpressoTable;
use WWW::Mechanize;
require Exporter;
our @ISA = qw(Exporter);
our @EXPORT = qw(PrintTop PrintBottom TLRTable SimpleList CreateFlipPageInterface ParseInputFields ParseSearchString CreateTargetInterface CreateQueryDisplay CreateKeywordInterface CreateCategoryInterface CreateLiteratureInterface CreateKeywordSpecInterface CreateSearchScopeInterface CreateSearchModeInterface CreateSortByInterface CreateParameterSettingInterface CreateCommandTextArea CreateCommandExplanations CreateDisplayOptions CreateDispEpp makeentry PrintStopwordWarning PrintTypeTabs PrintGlobalLinkTable gettext getsentences preparesortresults makehighlightterms CreateFilterInterface Filter FilterSearch);
sub PrintTop {
my $query = shift;
my $myself = shift;
my $menuflag = shift;
my $location = "";
foreach my $key (keys % { (HTML_MENU) }) {
my $aux = (HTML_MENU)->{$key};
$aux =~ s/\//\\\//;
if ($myself =~ /$aux/) {
$location = $key;
}
}
print $query->header(-cookie => [@_]);
my $javascript = <<JSEND;
function openlinkwin(NM, X ,Y, ST) {
Y = Y - 24;
var prop = "left=" + X + ",top=" + Y;
prop = prop + ",width=300,height=150,status=no,toolbar=no,menubar=no,scrollbars=no";
linkWin = window.open("", NM, prop);
linkWin.document.write("<HTML><head><title>Multiple Links</title></head>");
linkWin.document.write ("<BODY>");
var line = "Multiple links for \'" + NM + "\' found; please choose:<p>";
linkWin.document.write (line);
linkWin.document.write (ST);
linkWin.document.write ("</BODY></HTML>");
linkWin.document.close();
}
function closelinkwin() {
if (!linkWin.closed)
linkWin.self.close();
}
//Cloning Fields
var counter = 0;
function init() {
document.getElementById('moreFields').onclick = moreFields;
moreFields();
}
function moreFields() {
counter++;
var newFields = document.getElementById('readroot').cloneNode(true);
newFields.id = '';
newFields.style.display = 'block';
var newField = newFields.childNodes;
for (var i=0;i<newField.length;i++) {
var theName = newField[i].name
if (theName)
newField[i].name = theName + counter;
}
var insertHere = document.getElementById('writeroot');
insertHere.parentNode.insertBefore(newFields,insertHere);
window.onload = moreFields;
}
JSEND
my $css_style = '<!--
.TextField {
padding: 2px;
height: 14px;
border: 1px solid #CCCCCC;
}
-->';
print $query->start_html(-title => $location,
-author => DSP_AUTHOR,
-script => [
{-src => 'http://tetramer.tamu.edu/textpresso/scripts/jquery.idTabs.min.js'},
{-code => $javascript}],
-style => {-code => $css_style},
-text => DSP_TXTCOLOR,
-link => DSP_LNKCOLOR,
-vlink => DSP_LNKCOLOR,
-bgcolor => DSP_BGCOLOR);
if ($menuflag) {
my @menu = keys % { (HTML_MENU) };
for (my $i = 0; $i < @menu; $i++) {
my $link = (HTML_ROOT) . (HTML_MENU)->{$menu[$i]};
if ($menu[$i] =~ /^$location$/) {
my $clr = (DSP_HIGHLIGHT_COLOR)->{menutexton};
$menu[$i] = "<span style='font-weight:bold;color:#FDC867'>" . $menu[$i] . "</span>";
} else {
my $clr = (DSP_HIGHLIGHT_COLOR)->{menutextoff};
$menu[$i] = "<span style='font-weight:normal;color:white;text-decoration:none;'>" . $menu[$i] . "</span>";
}
$menu[$i] = "<a href='$link' style='text-decoration: none'>" . $menu[$i] . "</a>";
}
my $main_menu = new TextpressoTable;
$main_menu->init;
$main_menu->addtablerow(@menu);
my $wrap = new TextpressoTable;
$wrap->init;
$wrap->addtablerow($query->img({ -src => HTML_ROOT . HTML_LOGO,
-border => 0}));
my $wrap2 = new TextpressoTable;
$wrap2->init;
$wrap2->addtablerow($main_menu->maketable($query,
tablestyle => 'seamless',
width => '50%',
align => 'left',
DSP_HDRBCKGRND => 'black',
DSP_HDRSIZE => 'small'));
print $wrap->maketable($query, tablestyle => 'seamless', DSP_HDRBCKGRND => '#2F6798', width => "100%", align => 'left');
print $wrap2->maketable($query, tablestyle => 'seamless', DSP_HDRBCKGRND => 'black', width => "100%", align => 'left');
}
print $query->start_center;
# print $query->img({ -src => HTML_ROOT . HTML_LOGO,
# -border => 0});
print $query->end_center;
return $location;
}
sub PrintBottom {
my $query = shift;
my $extramessage = shift;
my $year = (localtime)[5] + 1900;
print $query->start_center;
print $query->p;
printf $query->span({-style=>"font-size:x-small;"}, "© Textpresso $year - ", $query->a({-href => 'about_textpresso'},
$query->span({-style => "background:white;color:#001EC9;font-size:x-small;text-decoration:underline;"}, "About Textpresso")));
print $query->span({-style=>"font-size:x-small;"}, $extramessage) if ($extramessage ne '');
print $query->end_html;
print $query->end_center;
}
sub TLRTable { # stands for Top-(Left-Right) Table
my $query = shift;
my $top = shift;
my $left = shift;
my $right = shift;
my $width = shift;
my $returnstring = "";
my $auxtb = new TextpressoTable;
$auxtb->init;
$auxtb->addtablerow(""); # no header, please
$auxtb->addtablerow($top);
$returnstring = $auxtb->maketable($query,
tablestyle => 'borderless',
width => $width);
$auxtb->init;
$auxtb->addtablerow(""); # no header, please
$auxtb->addtablerow($left, $right);
$returnstring .= $auxtb->maketable($query,
tablestyle => 'borderless',
width => $width);
return $returnstring;
}
sub SimpleList { # made with table
my $query = shift;
my $returnstring = "";
my $auxtb = new TextpressoTable;
$auxtb->init;
foreach (@_) {
$auxtb->addtablerow($_);
}
return $auxtb->maketable($query,
tablestyle => 'borderless',
DSP_HDRCOLOR => 'black',
DSP_HDRSIZE => 'small',
width => '100%');
}
sub generateweblinks {
my $query = shift;
my $string = shift;
my $output = $string;
my $on = shift;
my $p_urls = shift;
my $p_regexps = shift;
my $p_explanations = shift;
my @urls = @$p_urls; my @regexps = @$p_regexps; my @explanations = @$p_explanations;
if (!$on) {
return $output;
}
my %foundterms = ();
for (my $i=0; $i < @regexps; $i++) {
my @matches;
while ($string =~ /($regexps[$i])/g) {
push (@matches, $1);
}
if (@matches) {
foreach my $match (@matches) {
if (!($match eq "")) {
$foundterms{$match}{$i} = 1;
}
}
}
}
foreach my $term (keys % foundterms) {
my $target;
my @nmbs = keys % {$foundterms{$term}};
if (scalar(@nmbs) < 2) {
(my $suburl = $urls[$nmbs[0]]) =~ s/\#\#\#/$term/;
my $e = $explanations[$nmbs[0]];
$target = $query->a({href=>$suburl, -target=>"_blank",
title=>"Link to $e",
style=>'text-decoration:none'}, " $term ");
} else {
my $e = "<p>";
foreach my $inst (@nmbs) {
(my $auxurl = $urls[$inst]) =~ s/\#\#\#/$term/;
$e .= "<a href='" . $auxurl . "' target='_blank'>";
$e .= $explanations[$inst];
$e .= "</a><br>";
}
my $here = rand() . rand();
$target = $query->a({href=>"#here", target =>"_self", # anchor 'here' does not exist, so page stays where it is (hopefully).
onClick=>"openlinkwin(\"$term\", event.screenX, event.screenY,\"$e\")",
style=>'text-decoration:none'}, $term);
}
$output =~ s/(^| )$term( |$)/ $target /g;
}
return $output;
}
sub CreateFlipPageInterface {
my $query = shift;
my $prev = shift;
my $selector = shift;
my $next = shift;
my $displaypage = shift;
my @choices = @_;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("");
# $aux->addtablerow("Goto:");
my @row = ();
if ($prev) {
push @row, $query->submit(-name => 'previouspage', -value => 'Previous')
. $query->font(" ");
}
if ($selector) {
push @row,$query->font(" ")
. $query->submit(-name => 'gotopage', -value => 'Page')
. $query->textfield(-name =>'page',
-default => $displaypage,
-size => 5,
-values => \@choices
)
. $query->font(" of", scalar @choices)
. $query->font(" ");
}
if ($next) {
push @row, $query->font(" ") .
$query->submit(-name => 'nextpage', -value => 'Next');
}
$aux->addtablerow(@row);
return $aux->maketable($query, tablestyle => 'borderless', valign => 'middle');
}
sub ParseInputFields {
my $query = shift;
my $stopwordstring = shift;
my $tpquery = new TextpressoDatabaseQuery;
$tpquery->init;
my %literatures = ();
foreach ($query->param('literature')) {
$literatures{$_} = 1;
}
#
my %targets = ();
foreach ($query->param('target')) {
$targets{$_} = 1;
}
foreach ($query->param('target1')) {
$targets{$_} = 1;
}
foreach ($query->param('target2')) {
$targets{$_} = 1;
}
foreach ($query->param('target3')) {
$targets{$_} = 1;
}
foreach ($query->param('target4')) {
$targets{$_} = 1;
}
#
for (my $i = 1; $i < 5; $i++) {
if ($query->param("cat$i") ne HTML_NONE) {
my $aux = (DB_CATEGORIES)->{$query->param("cat$i")};
if (defined(@{(DB_CATEGORYCHILDREN)->{$query->param("cat$i")}})) {
foreach my $child (@{(DB_CATEGORYCHILDREN)->{$query->param("cat$i")}}) {
$aux .= "," . (DB_CATEGORIES)->{$child};
}
}
$tpquery->addsimple('category', $aux,
$query->param('sentencerange'), $query->param('exactmatch') || 0,
$query->param('casesensitive') || 0, \%literatures, \%targets);
}
}
#
my $foundstopwords = ParseSearchString($query->param('searchstring'), $tpquery, $stopwordstring, 0, '>',
$query->param('sentencerange'), $query->param('exactmatch') || 0,
$query->param('casesensitive') || 0, \%literatures, \%targets);
#
return ($tpquery, $foundstopwords);
}
sub ParseSearchString {
my $string = shift;
my $tpquery = shift;
my $stopwordstring = shift;
my $num = shift;
my $comp = shift;
my $range = shift;
my $exactmatch = shift;
my $casesensitive = shift;
my $pLit = shift;
my $pTgt = shift;
my $foundstopwords = "";
my @plusphrases = ();
while ($string =~ /(\s|^)\"([^\"]+)\"(\s|$)/g) {
push @plusphrases, $2;
$string =~ s/\"$2\"//;
}
my @minusphrases = ();
while ($string =~ /(\s|^)\-\"([^\"]+)\"(\s|$)/g) {
push @minusphrases, $2;
$string =~ s/\-\"$2\"//;
}
my @minuswords = ();
while ($string =~ /(\s|^)\-(\S+?)(\s|$)/g) {
push @minuswords, $2;
$string =~ s/\-$2//;
}
my @pluswords = ();
while ($string =~ /(\s|^)(\S+?)(\s|$)/g) {
push @pluswords, $2;
$string =~ s/$2//;
}
foreach my $line (@plusphrases) {
my @entries = split(/\s/, $line);
my $aux = shift(@entries);
if ($stopwordstring =~ /\s$aux\s/) {
$foundstopwords .= $aux . " ";
} else {
$tpquery->addspecific('&&', 'keyword', $aux, $num, $comp, $range, $exactmatch, $casesensitive, $pLit, $pTgt);
}
while (my $word = shift(@entries)) {
if ($stopwordstring =~ /\s$word\s/) {
$foundstopwords .= $word . " ";
} else {
$tpquery->addspecific('++', 'keyword', $word, $num, $comp, $range, $exactmatch, $casesensitive, $pLit, $pTgt);
}
}
}
foreach my $word (@pluswords) {
if ($stopwordstring =~ /\s$word\s/) {
$foundstopwords .= $word . " ";
} else {
$tpquery->addspecific('&&', 'keyword', $word, $num, $comp, $range, $exactmatch, $casesensitive, $pLit, $pTgt);
}
}
foreach my $line (@minusphrases) {
my @entries = split(/\s/, $line);
my $aux = shift(@entries);
if ($stopwordstring =~ /\s$aux\s/) {
$foundstopwords .= $aux . " ";
} else {
$tpquery->addspecific('!!', 'keyword', $aux, $num, $comp, $range, $exactmatch, $casesensitive, $pLit, $pTgt);
}
while (my $word = shift(@entries)) {
if ($stopwordstring =~ /\s$word\s/) {
$foundstopwords .= $word . " ";
} else {
$tpquery->addspecific('--', 'keyword', $word, $num, $comp, $range, $exactmatch, $casesensitive, $pLit, $pTgt);
}
}
}
foreach my $word (@minuswords) {
if ($stopwordstring =~ /\s$word\s/) {
$foundstopwords .= $word . " ";
} else {
$tpquery->addspecific('!!', 'keyword', $word, $num, $comp, $range, $exactmatch, $casesensitive, $pLit, $pTgt);
}
}
return $foundstopwords;
}
sub CreateQueryDisplay {
my $query = shift;
my $tpquery = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("Query");
$aux->addtablerow("Condition",
"Concatenation",
"Type",
"Data Entry",
"Comparison",
"Numerics",
"Sentence Range",
"Exact Match?",
"Case Sensitive?",
"Literatures",
"Fields");
for (my $i = 0; $i < $tpquery->numberofconditions; $i++) {
my $matchanswer = ($tpquery->exactmatch($i) == 1) ? 'yes' : 'no';
my $caseanswer = ($tpquery->casesensitive($i) == 1) ? 'yes' : 'no';
$aux->addtablerow($i,
$tpquery->boolean($i),
$tpquery->type($i),
$tpquery->data($i),
$tpquery->comparison($i),
$tpquery->occurrence($i),
$tpquery->range($i),
($tpquery->exactmatch($i)) ? 'yes' : 'no',
($tpquery->casesensitive($i)) ? 'yes' : 'no',
join(", ", $tpquery->literatures($i)),
join(", ", $tpquery->targets($i)));
}
return $aux->maketable($query,
tablestyle => 'borderless-headerbackground',
DSP_HDRBCKGRND => (DSP_HIGHLIGHT_COLOR)->{bgwhite},
DSP_HDRCOLOR => 'black');
}
sub CreateDispEpp {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
my @sortchoice = qw(5 10 20 50);
$aux->addtablerow("Show ". $query->popup_menu(-name => 'disp_epp',
-onChange => q/document.getElementById('main_form').submit()/,
-values => [@sortchoice],
-default => '5',
));
return $aux->maketable($query,
tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small',
width => '100%');
}
sub CreateKeywordInterface {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("for " . $query->textfield(-name => 'searchstring', -size => 50, -maxlength => 255),
$query->submit(-name => 'search', -value => 'Go')
. $query->font(" ")
. $query->reset('Clear'));
# $aux->addtablerow("Separate multiple, <em>required</em> keywords by white spaces (Boolean \'and\').");
# $aux->addtablerow("Separate multiple, <em>alternative</em> keywords by a comma with no white spaces (Boolean \'or\').");
# $aux->addtablerow("Enter phrases in double quotes, and put a '-' sign in front of words which are to be excluded.");
return $aux->maketable($query,
tablestyle => 'borderless', DSP_BGCOLOR => '#CCCCCC',# DSP_HDRCOLOR => '#FDC867',
DSP_HDRSIZE => 'small', align => 'left',
width => '100%');
}
sub FilterSearch {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow($query->span({-style => 'font-weight:normal;color:white;'}, "title of article:"),
$query->textfield(-name => 'titlestring', -size => 50, -maxlength => 255));
$aux->addtablerow($query->span({-style => 'font-weight:normal;color:white;'}, "author(s):"),
$query->textfield(-name => 'authorstring', -size => 50, -maxlength => 255));
$aux->addtablerow($query->span({-style => 'font-weight:normal;color:white;'}, "publication date:"),
$query->textfield(-name => 'yearstring', -size => 50, -maxlength => 255));
$aux->addtablerow($query->span({-style => 'font-weight:normal;color:white;'}, "type (e.g. review):"),
$query->textfield(-name => 'typestring', -size => 50, -maxlength => 255));
$aux->addtablerow($query->span({-style => 'font-weight:normal;color:white;'}, "journal name:"),
$query->textfield(-name => 'journalstring', -size => 50, -maxlength => 255));
$aux->addtablerow($query->span({-style => 'font-weight:normal;color:white;'}, "mesh headings:"),
$query->textfield(-name => 'meshstring', -size => 50, -maxlength => 255));
return $aux->maketable($query,
tablestyle => 'borderless', DSP_BGCOLOR => '#2F6798', DSP_HDRCOLOR => '#FDC867',
DSP_HDRSIZE => 'small', align => 'right',
width => '100%');
}
sub CreateFilterInterface {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("Narrow your search results with filter:");
$aux->addtablerow($query->textfield(-name => 'filterstring', -size => 50, -maxlength => 255) . " " .
$query->submit(-name => 'filter', -value => 'Filter!'));
$aux->addtablerow("Put a '+' sign in front of words which have to be included,\
a '-' sign in front of words which have to be excluded. \
Enter the field of the word, <em>viz</em> author, title, \
year, journal, abstract, accession, type or sentence \
in square brackets. Enter phrases in double quotes.");
$aux->addtablerow("For example, to find all the papers in the search result \
that have <em>Jack</em> as author,
but not <em>John</em>, enter \+Jack\-John\[author\]\. \
To exclude all papers that have the phrase <em>double mutant</em> \
in title, enter \-\"double mutant\"\[title\].
You can combine several filters and enter something like
+Kim[author] \-\"double mutant\"\[title\] +15943900[accession] +2005[year] -review\[type\]. ");
$aux->addtablerow("Click on Filter! button to activate the filter.");
return $aux->maketable($query,
tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small',
width => '100%');
}
sub CreateCategoryInterface {
my $query = shift;
# my $aux = new TextpressoTable;
# $aux->init;
use TextpressoDatabaseCategories;
my $none = HTML_NONE;
my @categories = sort ($none, keys %{(DB_CATEGORIES)});
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("Categories:");
$aux->addtablerow($query->popup_menu(-name => 'cat1',
-values => [sort @categories],
-default => $none));
$aux->addtablerow($query->popup_menu(-name => 'cat2',
-values => [sort @categories],
-default => $none));
$aux->addtablerow($query->popup_menu(-name => 'cat3',
-values => [sort @categories],
-default => $none));
$aux->addtablerow($query->popup_menu(-name => 'cat4',
-values => [sort @categories],
-default => $none));
# $aux->addtablerow($miniT->maketable($query, tablestyle => 'borderless', valign => 'middle'));
return $aux->maketable($query,
tablestyle => 'borderless',
DSP_HDRBCKGRND => '#2F6798', DSP_HDRCOLOR => '#FDC867', DSP_BGCOLOR => '#2F6798', align => 'left',
DSP_HDRSIZE => 'small',
width => '100%');
}
sub CreateLiteratureInterface {
my $query = shift;
my $error = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("Literature:");
$aux->addtablerow($query->checkbox_group(-name => 'literature',
-values => [sort keys %{(DB_LITERATURE)}],
-defaults => [@{(DB_LITERATURE_DEFAULTS)}],
-cols => 1));
return $aux->maketable($query,
tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small', DSP_HDRBCKGRND => $error || '#FDC867',
DSP_HDRBCKGRND => '#2F6798', DSP_HDRCOLOR => '#FDC867', DSP_BGCOLOR => '#2F6798', width => "100%", align => 'left',
width => '100%');
}
#sub CreateTargetInterface {
#
# my $query = shift;
# my $aux = new TextpressoTable;
# $aux->init;
# $aux->addtablerow("Fields");
# $aux->addtablerow($query->checkbox_group(-name => 'target',
# -values => [sort keys %{(DB_SEARCH_TARGETS)}],
# -defaults => [@{(DB_SEARCH_TARGETS_DEFAULTS)}],
# -rows => 2));
# return $aux->maketable($query,
# tablestyle => 'borderless-headerbackground',
# DSP_HDRSIZE => 'small',
# width => '100%');
#
#}
sub CreateTargetInterface {
my $query = shift;
my $aux = new TextpressoTable;
my @targets = sort (keys %{(DB_SEARCH_TARGETS)});
$aux->init;
# $aux->addtablerow($query->popup_menu(-name => 'target', -values => [sort @targets], -default => $targets[2],));
$aux->addtableelement('Search');
$aux->addtablerow($query->popup_menu(-name => 'target', -values => [sort @targets], -default => $targets[2],) .
$query->a({href=>'Javascript:moreFields()',
-style => 'font-weight:normal;color:#2F6798;text-decoration:none;'}, ' +') .
$query->span( {-id => 'writeroot'} ),
);
return $aux->maketable($query,
tablestyle => 'borderless',
DSP_HDRSIZE => 'small', DSP_BGCOLOR => '#CCCCCC',
width => '100%');
}
sub CreateKeywordSpecInterface {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
# $aux->addtablerow("Keyword Specifications:");
$aux->addtablerow($query->checkbox(-name => 'exactmatch',
-label => 'Exact match'));
$aux->addtablerow($query->checkbox(-name => 'casesensitive',
-label => 'Case sensitive'));
return $aux->maketable($query,
tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small',
DSP_HDRBCKGRND => '#CCCCCC', DSP_HDRCOLOR => 'black', DSP_BGCOLOR => '#CCCCCC', align => 'left',
width => '100%');
}
sub CreateSearchScopeInterface {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("Search Scope:");
$aux->addtablerow($query->popup_menu(-name => 'sentencerange',
-values => [sort keys %{(DB_SEARCH_RANGES)}],
-default => DB_SEARCH_RANGES_DEFAULT));
return $aux->maketable($query,
tablestyle => 'borderless',
DSP_HDRSIZE => 'small',
DSP_HDRBCKGRND => '#2F6798', DSP_HDRCOLOR => '#FDC867', DSP_BGCOLOR => '#2F6798', align => 'left',
width => '100%');
}
sub CreateSearchModeInterface {
my $query = shift;
my $error = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("Search Mode:");
$aux->addtablerow($query->popup_menu(-name => 'mode',
-values => [sort @{(DB_SEARCH_MODE)}],
-default => DB_SEARCH_MODE_DEFAULT));
return $aux->maketable($query,
tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small', DSP_HDRBCKGRND => $error || '#2F6798',
DSP_HDRCOLOR => '#FDC867', DSP_BGCOLOR => '#2F6798', width => "100%", align => 'left',
width => '100%');
}
sub CreateSortByInterface {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
my @sortchoice = sort ("Sort By", "score (hits)", keys % {(DB_DISPLAY_FIELDS)});
$aux->addtablerow($query->popup_menu(-name => 'sort',
-onChange => q/document.getElementById('main_form').submit()/,
-values => [@sortchoice],
-default => 'Sort By',
));
#-default => 'score (hits)',
return $aux->maketable($query,
tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small',
);
}
sub CreateParameterSettingInterface {
my $query = shift;
my $paramtable = new TextpressoTable;
$paramtable->init;
$paramtable->addtablerow("Parameter Settings");
$paramtable->addtablerow($query->span({-style => 'font-weight:bold;'}, "Literature(s): ") .
$query->span({-style => 'font-weight:normal;'}, join(", " , $query->param('literature'))));
$paramtable->addtablerow($query->span({-style => 'font-weight:bold;'}, "Field(s): ") .
$query->span({-style => 'font-weigt:normal;'}, join(", " , $query->param('target'),
$query->param('target1'),
$query->param('target2'),
$query->param('target3'),
$query->param('target4'),
)));
my $answer = ($query->param('exactmatch')) ? 'Yes' : 'No';
$paramtable->addtablerow($query->span({-style => 'font-weight:bold;'}, "Exact match? ") .
$query->span({-style => 'font-weigt:normal;'}, $answer));
$answer = ($query->param('casesensitive')) ? 'Yes' : 'No';
$paramtable->addtablerow($query->span({-style => 'font-weight:bold;'}, "Case sensitive? ") .
$query->span({-style => 'font-weigt:normal;'}, $answer));
$paramtable->addtablerow($query->span({-style => 'font-weight:bold;'}, "Sentence Scope: ") .
$query->span({-style => 'font-weigt:normal;'}, $query->param('sentencerange')));
$paramtable->addtablerow($query->span({-style => 'font-weight:bold;'}, "Search Mode: ") .
$query->span({-style => 'font-weigt:normal;'}, $query->param('mode')));
$paramtable->addtablerow($query->span({-style => 'font-weight:bold;'}, "Sorted by: ") .
$query->span({-style => 'font-weigt:normal;'}, $query->param('sort')));
return $paramtable->maketable($query, tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small', DSP_HDRBCKGRND => '#D5DDF1', width => "100%");
}
sub CreateCommandTextArea {
my $query = shift;
my $title = shift;
my $line1 = shift;
my $line2 = shift;
my $commandtable = new TextpressoTable;
$commandtable->init;
$commandtable->addtablerow("Commands");
$commandtable->addtablerow($query->span({-style => 'font-style:normal;'}, $line1) .
$query->span({-style => 'font-style:normal;'}, $line2));
$commandtable->addtablerow($query->textarea(-name => 'commands',
-rows => '8',
-columns => '50'));
$commandtable->addtablerow($query->submit(-name => 'submit',
-value => 'Submit!'));
return $commandtable->maketable($query, tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small', width => "100%");
}
sub CreateCommandExplanations {
my $query = shift;
my $history = shift;
my $explanation = new TextpressoTable;
$explanation->init;
$explanation->addtablerow("Explanations");
$explanation->addtablerow($query->span({-style => 'font-weight:bold;'}, "Available Commands:"));
$explanation->addtablerow($query->span({-style => 'font-style:italic;'}, "set ") .
$query->span({-style => 'font-style:normal;'}, "parameter-name ") .
$query->span({-style => 'font-style:italic;'}, "= ") .
$query->span({-style => 'font-style:normal;'}, "value-1, value-2, ... \'"));
$explanation->addtablerow($query->span({-style => 'font-style:italic;'}, "clear ") .
$query->span({-style => 'font-style:normal;'}, "(parameter-name | ") .
$query->span({-style => 'font-style:italic;'}, "all") .
$query->span({-style => 'font-style:normal;'}, ")"));
$explanation->addtablerow($query->span({-style => 'font-style:italic;'}, "find ") .
$query->span({-style => 'font-style:normal;'}, "(") .
$query->span({-style => 'font-style:italic;'}, "keyword ") .
$query->span({-style => 'font-style:normal;'}, "| ") .
$query->span({-style => 'font-style:italic;'}, "category") .
$query->span({-style => 'font-style:normal;'}, "| ") .
$query->span({-style => 'font-style:italic;'}, "attribute") .
$query->span({-style => 'font-style:normal;'}, ") (keyword | ") .
$query->span({-style => 'font-style:italic;'}, "\"") .
$query->span({-style => 'font-style:normal;'}, "phrase") .
$query->span({-style => 'font-style:italic;'}, "\"") .
$query->span({-style => 'font-style:normal;'}, " | category | category") .
$query->span({-style => 'font-style:italic;'}, ":") .
$query->span({-style => 'font-style:normal;'}, "attribute") .
$query->span({-style => 'font-style:italic;'}, ":") .
$query->span({-style => 'font-style:normal;'}, "value) (") .
$query->span({-style => 'font-style:italic;'}, "< ") .
$query->span({-style => 'font-style:normal;'}, "| ") .
$query->span({-style => 'font-style:italic;'}, "== ") .
$query->span({-style => 'font-style:normal;'}, "| ") .
$query->span({-style => 'font-style:italic;'}, ">") .
$query->span({-style => 'font-style:normal;'}, ") number ") .
$query->span({-style => 'font-style:italic;'}, "->") .
$query->span({-style => 'font-style:normal;'}, " variable-name"));
$explanation->addtablerow($query->span({-style => 'font-style:normal;'}, "(") .
$query->span({-style => 'font-style:italic;'}, "and ") .
$query->span({-style => 'font-style:normal;'}, "| ") .
$query->span({-style => 'font-style:italic;'}, "or ") .
$query->span({-style => 'font-style:normal;'}, "| ") .
$query->span({-style => 'font-style:italic;'}, "not") .
$query->span({-style => 'font-style:normal;'}, ") ") .
$query->span({-style => 'font-style:normal;'}, "variable-name-1 variable-name-2 ") .
$query->span({-style => 'font-style:italic;'}, "->") .
$query->span({-style => 'font-style:normal;'}, " variable-name-3"));
$explanation->addtablerow($query->span({-style => 'font-style:italic;'}, "display ") .
$query->span({-style => 'font-style:normal;'}, "variable-name"));
if ($history ne "") {
$explanation->addtablerow("");
$explanation->addtablerow($query->span({-style => 'font-weight:bold;'}, "Last Command(s):"));
$explanation->addtablerow($query->span({-style => 'font-style:normal;'}, $history));
}
return $explanation->maketable($query, tablestyle => 'borderless-headerbackground',
DSP_HDRSIZE => 'small', width => "100%", DSP_HDRBCKGRND => 'seagreen');
}
sub CreateDisplayOptions {
my $query = shift;
my $aux = new TextpressoTable;
$aux->init;
$aux->addtablerow("");
$aux->addtablerow($query->span({-style=>"font-size:small;"}, "Display options:"));
my $none = HTML_NONE;
my $on = HTML_ON;
my $off = HTML_OFF;
my @row = ();
my $count = 0;
my $selfurl = $query->self_url;
my $oncolor = (DSP_HIGHLIGHT_COLOR)->{oncolor};
my $offcolor = (DSP_HIGHLIGHT_COLOR)->{offcolor};
foreach my $opt (keys % {(DB_DISPLAY_FIELDS)}, 'supplementals', 'textlinks', 'searchterm-highlighting') {
my $entry = $opt . ': ';
if (!defined($query->param("disp_$opt"))) {
$query->param(-name => "disp_$opt", -value => $on);
$query->param(-name => "disp_mesh", -value => $off);
}
(my $actualurl = $selfurl) =~ s/disp_$opt=$on//g;
$actualurl =~ s/disp_$opt=$off//;
if ($query->param("disp_$opt") eq $on) {
$entry .= $query->start_b;
$entry .= $query->a({-href => "$actualurl\;disp_$opt=$on"}, $query->span({-style=>"font-size:small;color:$oncolor"}, $on));
$entry .= $query->end_b;
$entry .= $query->span({-style=>"font-size:small;"}, " | ");
$entry .= $query->a({-href => "$actualurl\;disp_$opt=$off"}, $query->span({-style=>"font-size:small;"}, $off));
} else {
$entry .= $query->a({-href => "$actualurl\;disp_$opt=$on"}, $query->span({-style=>"font-size:small;"}, $on));
$entry .= $query->span({-style=>"font-size:small;"}, " | ");
$entry .= $query->start_b;
$entry .= $query->a({-href => "$actualurl\;disp_$opt=$off"}, $query->span({-style=>"font-size:small;color:$offcolor"}, $off));
$entry .= $query->end_b;
}
push @row, $entry;
if ((++$count % 5) == 0) {
$aux->addtablerow(@row);
@row = ();
}
}
my $entry = "matching sentences: ";
if (!defined ($query->param("disp_matches"))) {
$query->param(-name => "disp_matches", -value => 1);
}
(my $actualurl = $selfurl) =~ s/disp_matches=($none|1|5|10)//g;
foreach my $opt ("$none", 1, 5, 10) {
my $str = "";
if ($query->param("disp_matches") == $opt) {
$entry .= $query->start_b;
$str = $query->span({-style=>"font-size:small;color:$oncolor"}, $opt);
} else {
$str = $opt;
}
$entry .= $query->a({-href => "$actualurl\;disp_matches=$opt"}, $query->span({-style=>"font-size:small;"}, $str));
$entry .= $query->span({-style=>"font-size:small;"}, " ");
if ($query->param("disp_matches") == $opt) {
$entry .= $query->end_b;
}
}
push @row, $entry;
if ((++$count % 5) == 0) {
$aux->addtablerow(@row);
@row = ();
}
$entry = "entries/page: ";
if (!defined($query->param("disp_epp"))) {
$query->param(-name => "disp_epp", -value => 5);
}
($actualurl = $selfurl) =~ s/disp_epp=(5|10|20|50)//g;
foreach my $opt (5, 10, 20, 50) {
my $str = "";
if ($query->param("disp_epp") == $opt) {
$entry .= $query->start_b;
$str = $query->span({-style=>"font-size:small;color:$oncolor"}, $opt);
} else {
$str = $opt;
}
$entry .= $query->a({-href => "$actualurl\;disp_epp=$opt"}, $query->span({-style=>"font-size:small;"}, $str));
$entry .= $query->span({-style=>"font-size:small;"}, " ");
if ($query->param("disp_epp") == $opt) {
$entry .= $query->end_b;
}
}
#push @row, $entry;
$aux->addtablerow(@row);
return $aux->maketable($query, tablestyle => 'borderless', valign => 'middle');
}
sub makeentry {
my $query = shift;
my $table = shift;
my $ltk = shift;
my $pSEN = shift;
my $pResults = shift;
#############################
my $p_urls = shift;
my $p_regexps = shift;
my $p_explanations = shift;
#############################
my $var = shift;
(my $lit, my $tgt, my $key) = split(/\ -\ /, $ltk);
my $none = HTML_NONE;
my $on = HTML_ON;
my $leftcontent = "";
if ($query->param("disp_title") eq $on) {
my $pmid = $key;
my $title = highlighttext(generateweblinks($query, gettext($lit, 'title', $key),
($query->param("disp_textlinks") eq $on), $p_urls, $p_regexps, $p_explanations),
(DSP_HIGHLIGHT_COLOR)->{texthighlight},
$var);
if ($ENV{'REMOTE_ADDR'} =~ /^165\.91/) {
if (-e "/usr/local/textpresso/ecoli/Data/includes/pdf/$pmid.pdf") {
# $leftcontent = $query->span({-style => "font-weight:bold;"}, "Title: ");
$leftcontent .= $query->a({-href => "showpdf?filename=$pmid.pdf",
-target => "_blank"},
$query->span({-style => "font-weight:normal;font-size:medium;background:white;color:#001EC9;text-decoration:underline;"}, "$title"));
} else { $leftcontent = $query->span({-style => "font-size:medium;text-decoration:underline"},$title);
}
} else {
# $leftcontent = $title; #$query->span({-style => "font-weight:bold;"}, "Title: ") . $title;
$leftcontent = $query->span({-style => "font-size:medium;text-decoration:underline;"},$title);
}
}
$table->addtablerow($leftcontent);
if ($query->param("disp_author") eq $on) {
#$leftcontent = $query->span({-style => "font-weight:bold;"}, "Author: ") . gettext($lit, 'author', $key);
$leftcontent = $query->span({-style => "font-size:medium;"}, gettext($lit, 'author', $key));
$table->addtablerow($leftcontent);
}
$leftcontent = "";
if ($query->param("disp_journal") eq $on) {
#$leftcontent .= $query->span({-style => "font-weight:bold;"}, " Journal: ") . gettext($lit, 'journal', $key);
$leftcontent .= $query->span({-style => "font-size:small;"}, gettext($lit, 'journal', $key));
}
if ($query->param("disp_year") eq $on) {
# $leftcontent .= $query->span({-style => "font-weight:bold;"}, " Year: ") . gettext($lit, 'year', $key);
$leftcontent .= $query->span({-style => "font-size:small;"}, " " . gettext($lit, 'year', $key));
}
if ($query->param("disp_citation") eq $on) {
#$leftcontent .= $query->span({-style => "font-weight:bold;"}, " Citation: ") . gettext($lit, 'citation', $key);
$leftcontent .= $query->span({-style => "font-size:small;"}, gettext($lit, 'citation', $key));
}
my $aux = gettext($lit, 'type', $key);
if ($query->param("disp_type") eq $on) {
$leftcontent .= $query->span({-style => "font-weight:bold;"}, " Type: ") . $aux;
}
if ($aux =~ /(meeting|gazette)/i) {