function DisplayHtmlContent()
{
global $config;
global $db;
$this->display_disqus = false;
echo html_page_header(true, '', 'name');
echo '<h1>' . $this->GetTitle() . '</h1>';
echo '<h2>' . num_cited_by($this->id) . " citations" . '</h2>';
echo '<p class="explanation">References in BioStor that cite this reference</p>' . "\n";
$sql = 'SELECT DISTINCT(rdmp_reference_cites.reference_id) FROM rdmp_reference_citation_string_joiner
INNER JOIN rdmp_reference_cites USING(citation_string_id)
WHERE rdmp_reference_citation_string_joiner.reference_id=' . $this->id;
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
echo '<ul>' . "\n";
while (!$result->EOF) {
$reference = db_retrieve_reference($result->fields['reference_id']);
echo '<li style="border-bottom:1px dotted rgb(128,128,128);padding:4px;">';
echo '<a href="' . $config['web_root'] . 'reference/' . $result->fields['reference_id'] . '">' . $reference->title . '</a><br/>';
echo '<span style="color:green;">' . reference_authors_to_text_string($reference);
if (isset($reference->year)) {
echo ' (' . $reference->year . ')';
}
echo ' ' . reference_to_citation_text_string($reference) . '</span>';
echo ' ' . reference_to_coins($reference);
echo '</li>';
$result->MoveNext();
}
echo '</ul>' . "\n";
}
function DisplayHtmlContent()
{
global $config;
echo html_page_header(true, '', 'name');
echo '<div style="float:right;background-color:rgb(230,242,250);padding:6px">' . "\n";
if ($this->issn != '') {
echo '<h2>Identifiers</h2>' . "\n";
echo '<ul class="guid-list">' . "\n";
echo '<li class="permalink"><a href="' . $config['web_root'] . 'issn/' . $this->issn . '" title="Permalink">' . $config['web_root'] . 'issn/' . $this->issn . '</a></li>' . "\n";
echo '<li class="worldcat"><a href="http://www.worldcat.org/issn/' . $this->issn . '" title="ISSN">' . $this->issn . '</a></li>' . "\n";
echo '<h2>Export</h2>' . "\n";
echo '<ul class="export-list">' . "\n";
echo '<li class="xml"><a href="' . $config['web_root'] . 'issn/' . $this->issn . '.xml" title="Endnote XML">Endnote XML</a></li>';
echo '<li class="ris"><a href="' . $config['web_root'] . 'issn/' . $this->issn . '.ris" title="RIS">Reference manager</a></li>';
echo '<li class="bibtex"><a href="' . $config['web_root'] . 'issn/' . $this->issn . '.bib" title="BibTex">BibTex</a></li>';
echo '<li class="text"><a href="' . $config['web_root'] . 'issn/' . $this->issn . '.text" title="text">Text</a></li>';
echo '</ul>' . "\n";
}
if ($this->oclc != '') {
echo '<h2>Identifiers</h2>' . "\n";
echo '<ul class="guid-list">' . "\n";
echo '<li class="permalink"><a href="' . $config['web_root'] . 'oclc/' . $this->oclc . '" title="Permalink">' . $config['web_root'] . 'oclc/' . $this->oclc . '</a></li>' . "\n";
echo '<li class="worldcat"><a href="http://www.worldcat.org/oclc/' . $this->oclc . '" title="OCLC">' . $this->oclc . '</a></li>' . "\n";
echo '<h2>Export</h2>' . "\n";
echo '<ul class="export-list">' . "\n";
echo '<li class="xml"><a href="' . $config['web_root'] . 'oclc/' . $this->oclc . '.xml" title="Endnote XML">Endnote XML</a></li>';
echo '<li class="ris"><a href="' . $config['web_root'] . 'oclc/' . $this->oclc . '.ris" title="RIS">Reference manager</a></li>';
echo '<li class="bibtex"><a href="' . $config['web_root'] . 'oclc/' . $this->oclc . '.bib" title="BibTex">BibTex</a></li>';
echo '<li class="text"><a href="' . $config['web_root'] . 'oclc/' . $this->oclc . '.text" title="text">Text</a></li>';
echo '</ul>' . "\n";
}
echo '</div>' . "\n";
echo '<h1>' . $this->GetTitle() . '</h1>';
// Image
if (isset($this->issn)) {
echo '<div>';
echo '<img src="http://bioguid.info/issn/image.php?issn=' . $this->issn . '" alt="cover" style="border:1px solid rgb(228,228,228);height:100px;" />';
echo '</div>';
}
// Stats
/* echo '<div>';
echo '<img src="' . sparkline_articles_added_for_issn($this->issn) . '" alt="sparkline" />';
echo '</div>';*/
echo '<a href="http://twitter.com/share" class="twitter-share-button" data-count="vertical" data-via="rdmpage" data-related="biostor_org">Tweet</a><script type="text/javascript" src="http://platform.twitter.com/widgets.js"></script>';
echo '<h2>Coverage</h2>' . "\n";
echo '<p>';
if ($this->issn != '') {
echo bhl_articles_for_issn($this->issn);
}
if ($this->oclc != '') {
echo bhl_articles_for_oclc($this->oclc);
}
echo ' articles in database.</p>' . "\n";
echo '<h3>Distribution of identified articles over time</h3>' . "\n";
echo '<div>' . "\n";
echo ' <img src="' . sparkline_references($this->issn, $this->oclc, 360, 100) . '" alt="sparkline" />' . "\n";
echo '</div>' . "\n";
$titles = array();
if ($this->issn != '') {
$titles = bhl_titles_for_issn($this->issn);
}
if ($this->oclc != '') {
$titles = bhl_titles_for_oclc($this->oclc);
}
if (count($titles) > 0) {
echo '<h3>Distribution of identified articles across BHL items</h3>' . "\n";
echo '<div>';
echo '<div style="display:inline;background-color:rgb(230,242,250);width:20px;height:20px;"> </div>';
echo ' Scanned pages ';
echo '<div style="display:inline;background-color:rgb(0,119,204);width:10px;height:10px;"> </div>';
echo ' Articles ';
echo '</div>';
echo '<p></p>';
$items = array();
$volumes = array();
items_from_titles($titles, $items, $volumes);
$html = '<div style="height:400px;border:1px solid rgb(192,192,192);overflow:auto;">' . "\n";
$html .= '<table>' . "\n";
$html .= '<tbody style="font-size:10px;">' . "\n";
foreach ($volumes as $volume) {
$item = $items[$volume];
// How many pages in this item?
$num_pages = bhl_num_pages_in_item($item->ItemID);
// Coverage
$coverage = bhl_item_page_coverage($item->ItemID);
$row_height = 10;
// Draw as DIV
$html .= '<tr>' . "\n";
$html .= '<td>';
$html .= '<a href="http://www.biodiversitylibrary.org/item/' . $item->ItemID . '" target="_new">';
$html .= $item->VolumeInfo;
$html .= '</a>';
$html .= '</td>' . "\n";
$html .= '<td>' . "\n";
$html .= '<div style="position:relative">' . "\n";
$html .= ' <div style="background-color:rgb(230,242,250);border-bottom:1px solid rgb(192,192,192);border-right:1px solid rgb(192,192,192);position:absolute;left:0px;top:0px;width:' . $num_pages . 'px;height:' . $row_height . 'px;">' . "\n";
foreach ($coverage as $c) {
$html .= ' <div style="background-color:rgb(0,119,204);position:absolute;left:' . $c->start . 'px;top:0px;width:' . ($c->end - $c->start) . 'px;height:' . $row_height . 'px;">' . "\n";
$html .= ' </div>' . "\n";
}
$html .= ' </div>' . "\n";
$html .= '</div>' . "\n";
$html .= '</td>' . "\n";
$html .= '</tr>' . "\n";
}
$html .= '</tbody>' . "\n";
$html .= '</table>' . "\n";
$html .= '</div>' . "\n";
echo $html;
}
$institutions = institutions_from_titles($titles);
if (count($institutions) != 0) {
echo '<h3>BHL source(s)</h3>' . "\n";
echo '<table>' . "\n";
foreach ($institutions as $k => $v) {
echo '<tr>' . "\n";
echo '<td>' . "\n";
switch ($k) {
case 'American Museum of Natural History Library':
echo '<img src="' . $config['web_root'] . 'images/institutions/' . 'AMNH_logo_--_blue_rectangle.jpg' . '" width="48" />';
break;
case 'Harvard University, MCZ, Ernst Mayr Library':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'Mod_Color_Harvard_Shield_small_bigger.jpg' . '" width="48" />';
break;
case 'Missouri Botanical Garden':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'twitter_icon_MBG.jpg' . '" width="48" />';
break;
case 'New York Botanical Garden':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'NYBGDOMEHEADERWEB.jpg' . '" />';
break;
case 'Smithsonian Institution Libraries':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'SILCatesbyMagnolia.jpg' . '" width="48" />';
break;
case 'The Field Museum':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'field.jpg' . '" width="48" />';
break;
case 'BHL-Europe':
echo '<br /><div style="background-color:green;width:120px;text-align:center"><img src="' . $config['web_root'] . 'images/institutions/' . 'BHL_logo_wg.png' . '" height="48" /></div>';
break;
case 'Boston Public Library':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'BPLcards.jpg' . '" width="48" />';
break;
case 'Harvard University Herbarium':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'huh_logo_bw_100.png' . '" width="48" />';
break;
case 'MBLWHOI Library':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'library_logo2_bigger.jpg' . '" width="48" />';
break;
case 'Natural History Museum, London':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'natural_history_museum-01.jpg' . '" width="48" />';
break;
case 'University of Illinois Urbana Champaign':
echo '<br /><img src="' . $config['web_root'] . 'images/institutions/' . 'ilogo_horz_bold.gif' . '" height="48" />';
break;
default:
break;
}
echo '</td>' . "\n";
echo '<td>' . "\n";
echo $k . '<br />' . $v . ' items';
echo '</td>' . "\n";
echo '</tr>' . "\n";
}
echo '</table>' . "\n";
}
// How does journal relate to BHL Titles and Items?
$titles = array();
if ($this->issn != '') {
$titles = db_retrieve_journal_names_from_issn($this->issn);
}
if ($this->oclc != '') {
$titles = db_retrieve_journal_names_from_oclc($this->oclc);
}
if (count($titles) > 1) {
echo '<h2>Alternative titles</h2>';
echo '<ul>';
foreach ($titles as $title) {
echo '<li>' . $title . '</li>';
}
echo '</ul>';
}
echo '<h2>Articles</h2>';
if ($this->issn == '0374-5481') {
// Special treatment for Ann mag Nat Hist
echo '<ul>';
for ($series = 1; $series <= 9; $series++) {
echo '<li><a href="' . $config['web_root'] . 'issn/' . $this->issn . '#series' . $series . '">Series ' . $series . '</a></li>';
}
echo '</ul>';
for ($series = 1; $series <= 9; $series++) {
echo '<h3><a name="series' . $series . '"></a>Series ' . $series . '</h3>' . "\n";
$articles = db_retrieve_articles_from_journal_series($this->issn, $series == 1 ? '' : $series);
echo '<ul>';
foreach ($articles as $k => $v) {
echo '<li style="display:block;border-top:1px solid #EEE; ">' . $k;
echo '<ul>';
if (is_array($v)) {
foreach ($v as $ref) {
echo '<li><a href="' . $config['web_root'] . 'reference/' . $ref->id . '">' . $ref->title . '</a></li>';
}
}
echo '</ul>';
echo '</li>';
}
echo '</ul>';
}
} else {
$articles = db_retrieve_articles_from_journal($this->issn, $this->oclc);
//print_r($articles);
echo '<ul>';
foreach ($articles as $k => $v) {
echo '<li style="display:block;border-top:1px solid #EEE; ">' . $k;
echo '<ul>';
if (is_array($v)) {
foreach ($v as $ref) {
if (0) {
// fast
echo '<li><a href="' . $config['web_root'] . 'reference/' . $ref->id . '">' . $ref->title . '</a></li>';
} else {
// slower, but useful for debugging
$reference = db_retrieve_reference($ref->id);
echo '<li style="border-bottom:1px dotted rgb(128,128,128);padding:4px;">';
echo '<a href="' . $config['web_root'] . 'reference/' . $ref->id . '">' . $reference->title . '</a><br/>';
echo '<span style="color:green;">' . reference_authors_to_text_string($reference);
if (isset($reference->year)) {
echo ' (' . $reference->year . ')';
}
echo ' ' . reference_to_citation_text_string($reference) . '</span>';
echo ' ' . reference_to_coins($reference);
// Thumbail, useful for debugging
if (0) {
echo '<div>';
$pages = bhl_retrieve_reference_pages($ref->id);
$image = bhl_fetch_page_image($pages[0]->PageID);
echo '<a href="' . $config['web_root'] . 'reference/' . $ref->id . '">';
echo '<img style="padding:2px;border:1px solid blue;margin:2px;" id="thumbnail_image_' . $page->PageID . '" src="' . $image->thumbnail->url . '" width="' . $image->thumbnail->width . '" height="' . $image->thumbnail->height . '" alt="thumbnail"/>';
echo '</a>';
echo '</div>';
}
echo '</li>';
}
}
} else {
// Article lacks volume
if (isset($v->id)) {
$reference = db_retrieve_reference($v->id);
echo '<li style="border-bottom:1px dotted rgb(128,128,128);padding:4px;">';
echo '<a href="' . $config['web_root'] . 'reference/' . $v->id . '">' . $reference->title . '</a><br/>';
echo '<span style="color:green;">' . reference_authors_to_text_string($reference);
if (isset($reference->year)) {
echo ' (' . $reference->year . ')';
}
echo ' ' . reference_to_citation_text_string($reference) . '</span>';
echo ' ' . reference_to_coins($reference);
}
}
echo '</ul>';
echo '</li>';
}
echo '</ul>';
}
}
function display_article_metadata($reference)
{
// Metadata --------------------------------------------------------------------------
if (isset($reference->journal)) {
echo $reference->journal->name;
if (isset($reference->journal->series)) {
echo ' series ' . $reference->journal->series;
}
if (isset($reference->date)) {
switch (count($reference->date)) {
case 3:
echo ' ' . date('j F Y', strtotime(join('-', $reference->date)));
break;
case 2:
// Set date to first of month, but only show month
echo ' ' . date('F Y', strtotime(join('-', $reference->date) . '-01'));
break;
case 1:
echo ' ' . $reference->date[0];
break;
default:
break;
}
} else {
if (isset($reference->year)) {
echo ' ' . $reference->year;
}
}
if (isset($reference->journal->volume)) {
echo ' ' . $reference->journal->volume;
}
if (isset($reference->journal->issue)) {
echo '(' . $reference->journal->issue . ')';
}
if (isset($reference->journal->pages)) {
echo ':' . str_replace('--', '-', $reference->journal->pages);
}
echo '<br />';
}
if (isset($reference->identifier)) {
foreach ($reference->identifier as $identifier) {
switch ($identifier->type) {
case 'doi':
/*
echo 'DOI: ';
echo ' <a href="http://dx.doi.org/' . $identifier->id . '" target="_new"></i>' . $identifier->id . ' <span class="glyphicon glyphicon-new-window" aria-hidden="true"></span></a>';
echo '<br />';
*/
echo '<span class="doi"><a href="http://dx.doi.org/' . $identifier->id . '" target="_new">' . $identifier->id . '</a></span>';
echo '<br />';
break;
case 'jstor':
echo ' <span class="jstor"><a href="http://www.jstor.org/stable/' . $identifier->id . '" target="_new">' . $identifier->id . '</a></span>';
echo '<br />';
break;
case 'lsid':
echo '<span class="lsid"><a href="http://lsid.tdwg.org/' . $identifier->id . '" target="_new">' . $identifier->id . '</a></span>';
echo '<br />';
break;
default:
break;
}
}
}
// Title -----------------------------------------------------------------------------
echo "<h3>" . $reference->title . "</h3>";
// Authors ---------------------------------------------------------------------------
if (isset($reference->author)) {
if (count($reference->author) > 0) {
$authors = array();
foreach ($reference->author as $author) {
$string = '';
if (isset($author->firstname)) {
$string = $author->firstname . ' ' . $author->lastname;
} else {
$string = $author->name;
}
//$authors[] = '<a href="' . '?q=author:"' . $string . '"' . '">' . $string . '</a>';
$authors[] = '<a href="' . 'search/author:"' . $string . '"' . '">' . $string . '</a>';
}
echo join(', ', $authors);
}
}
// COinS -----------------------------------------------------------------------------
echo reference_to_coins($reference);
/*
echo '<pre>';
echo htmlentities(reference_to_google_scholar($reference));
echo '</pre>';
echo '<pre>';
echo htmlentities(reference_to_twitter($reference));
echo '</pre>';
echo '<pre>';
echo htmlentities(reference_to_coins($reference));
echo '</pre>';
echo '<pre>';
echo json_encode(reference_to_citeprocjs($reference), JSON_PRETTY_PRINT);
echo '</pre>';
*/
}
function DisplayHtmlContent()
{
global $config;
echo html_page_header(true, '', 'name');
echo '<h1>' . $this->GetTitle() . '</h1>';
if (count($this->object->specimens) == 0) {
echo '<p>No specimens with this code</p>';
} else {
// What articles have this specimen?
echo '<h2>References in BioStor with this specimen</h2>';
$refs = specimens_references_with_code($this->code);
//print_r($refs);
foreach ($refs as $occurrenceID => $ref_list) {
if ($occurrenceID != 0) {
echo '<p>GBIF occurrence <a class="gbif" href="http://data.gbif.org/occurrences/' . $occurrenceID . '/" target="_new">' . $occurrenceID . '</a>';
$datasetID = specimens_dataset_from_occurrence($occurrenceID);
$dataset = specimens_dataset($datasetID);
echo ' from dataset <a href="gbif_dataset.php?datasetID=' . $dataset->datasetID . '">' . $dataset->dataResourceName . ' (' . $dataset->providerName . ')' . '</a>';
echo '</p>';
$occurrence = specimens_from_occurrenceID($occurrenceID);
echo '<p>' . $occurrence->scientificName . ' (' . join(':', $occurrence->lineage) . ')' . '</p>';
} else {
echo '<p>(specimen not known in GBIF)</p>';
}
echo '<table cellspacing="0" cellpadding="2" width="100%">';
foreach ($ref_list as $reference_id) {
$reference = db_retrieve_reference($reference_id);
echo '<tr';
if (in_array($reference_id, $act_refs)) {
echo ' style="background-color:#D8F3C9;"';
}
echo '>';
if ($reference->PageID != 0) {
$image = bhl_fetch_page_image($reference->PageID);
$imageURL = $image->thumbnail->url;
} else {
// if it's an article we could use journal image
$imageURL = 'http://bioguid.info/issn/image.php?issn=' . $reference->issn;
}
echo '<td valign="top"><img style="border:1px solid rgb(192,192,192);" src="' . $imageURL . '" width="40" />';
echo '</td>';
echo '<td valign="top">';
echo '<a href="' . $config['web_root'] . 'reference/' . $reference_id . '">' . $reference->title . '</a><br/>';
echo '<span>' . reference_authors_to_text_string($reference);
if (isset($reference->year)) {
echo ' (' . $reference->year . ')';
}
echo ' ' . reference_to_citation_text_string($reference) . '</span>';
echo ' ' . reference_to_coins($reference);
if (0) {
echo '<div>';
echo bhl_pages_with_name_thumbnails($reference_id, $this->object->NameBankID);
echo '</div>';
}
echo '</td>';
echo '</tr>';
}
echo '</table>';
}
}
}
function display_search($text, $bookmark = '')
{
global $couch;
global $config;
$rows_per_page = 10;
$q = $text;
$q = str_replace(':', ',', $q);
if ($q == '') {
$obj = new stdclass();
$obj->rows = array();
$obj->total_rows = 0;
$obj->bookmark = '';
} else {
$url = '/_design/citation/_search/all?q=' . urlencode($q) . '&limit=' . $rows_per_page . '&include_docs=true';
if ($bookmark != '') {
$url .= '&bookmark=' . $bookmark;
}
$resp = $couch->send("GET", "/" . $config['couchdb_options']['database'] . "/" . $url);
$obj = json_decode($resp);
//print_r($config);
//echo $config['couchdb_options']['database'] . $url;
//exit();
}
echo '<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8"/>
<!-- Le styles -->
<link href="assets/css/bootstrap.css" rel="stylesheet">
<style type="text/css">
body {
padding-top: 60px;
padding-bottom: 40px;
}
.sidebar-nav {
padding: 9px 0;
}
.item-links a { margin-right:40px; }
</style>
<link href="assets/css/bootstrap-responsive.css" rel="stylesheet">
<link href="font-awesome.css" media="screen" rel="stylesheet" type="text/css" />
<!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
<!--[if lt IE 9]>
<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
</head>
<body>
<div class="navbar navbar-fixed-top">
<div class="navbar-inner">
<div class="container">
<a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</a>
<a class="brand" href=".">Biostor in the cloud</a>
<div class="nav-collapse">
<ul class="nav">
<li class="active"><a href=".">Home</a></li>
<li><a href="?page=about">About</a></li>
</ul>
</div><!--/.nav-collapse -->
<form class="navbar-search pull-left" method="get" action=".">
<input type="text" id=\'q\' name=\'q\' class="search-query" placeholder="Search" value="' . $q . '">
</form>
</div>
</div>
</div>
<div class="container-fluid">';
//print_r($obj);
if (isset($obj->error)) {
echo '<h3>Error</h3>';
echo '<p>' . $obj->reason . '</p>';
} else {
$total_rows = $obj->total_rows;
$bookmark = $obj->bookmark;
echo '<h3>' . $total_rows . ' hit(s)' . '</h3>';
if ($total_rows > $rows_per_page) {
echo '<p><a class="btn" href="?q=' . urlencode($q) . '&bookmark=' . $bookmark . '">More »</a></p>';
}
//echo '<p>' . "Bookmark=$bookmark " . '<a href="?q=' . urlencode($q) . '&bookmark=' . $bookmark . '">more</a>' . '</p>';
echo '<table class="table">';
echo '<thead>';
echo '</thead>';
echo '<tbody>';
foreach ($obj->rows as $row) {
$hit = $row->fields->default;
$reference = $row->doc;
$reference->id = $row->id;
echo '<tr>';
echo '<td style="text-align:center;width:100px;">';
if (isset($reference->thumbnail)) {
echo '<img style="box-shadow:2px 2px 2px #ccc;width:64px;" src="' . $reference->thumbnail . '">';
}
echo '</td>';
echo '<td class="item-data">';
//echo $row->order[0];
//echo '<p class="lead">';
echo '<p style="font-size:21px;font-weight:200;line-height:30px;">';
echo '<a href="id/' . $reference->id . '">' . $reference->title . '</a>';
echo '</p>';
echo '<div>';
if (isset($reference->year)) {
echo 'Published in <b>' . $reference->year . '</b>';
}
if (isset($reference->journal)) {
$issn = '';
if (isset($reference->journal->identifier)) {
foreach ($reference->journal->identifier as $identifier) {
if ($identifier->type == 'issn') {
$issn = $identifier->id;
}
}
}
if ($issn != '') {
echo ' in <b><a href="issn/' . $issn . '">' . $reference->journal->name . '</a></b>';
} else {
echo ' in <b>' . $reference->journal->name . '</b>';
}
if (isset($reference->journal->volume)) {
echo ', volume <b>' . $reference->journal->volume . '</b>';
}
if (isset($reference->journal->issue)) {
echo ', issue <b>' . $reference->journal->issue . '</b>';
}
if (isset($reference->journal->pages)) {
echo ', on pages <b>' . str_replace('--', '-', $reference->journal->pages) . '</b>';
}
} else {
// not a journal...
echo ', on pages <b>' . str_replace('--', '-', $reference->pages) . '</b>';
}
echo '</div>';
echo '<div>';
if (isset($reference->author)) {
$authors = array();
foreach ($reference->author as $author) {
if (isset($author->firstname)) {
$authors[] = $author->lastname . ' ' . $author->firstname;
} else {
$authors[] = $author->name;
}
}
echo join(', ', $authors);
}
echo '</div>';
// COinS
echo reference_to_coins($reference);
// Links
echo '<div class="item-links">';
//echo '<a href="">cite</a>';
if (isset($reference->identifier)) {
foreach ($reference->identifier as $identifier) {
switch ($identifier->type) {
case 'biostor':
echo '<a href="http://biostor.org/reference/' . $identifier->id . '" target="_new"><i class="icon-external-link"></i>biostor.org/reference/' . $identifier->id . '</a>';
break;
case 'cinii':
echo '<a href="http://ci.nii.ac.jp/naid/' . $identifier->id . '" target="_new"><i class="icon-external-link"></i>ci.nii.ac.jp/naid/' . $identifier->id . '</a>';
break;
case 'doi':
echo '<a href="http://dx.doi.org/' . $identifier->id . '" target="_new"><i class="icon-external-link"></i>doi.dx.org/' . $identifier->id . '</a>';
break;
case 'handle':
echo '<a href="http://hdl.handle.net/' . $identifier->id . '" target="_new"><i class="icon-external-link"></i>hdl.handle.net/' . $identifier->id . '</a>';
break;
case 'jstor':
echo '<a href="http://www.jstor.org/stable/' . $identifier->id . '" target="_new"><i class="icon-external-link"></i>www.jstor.org/stable/' . $identifier->id . '</a>';
break;
default:
break;
}
}
}
echo '</div>';
echo '</td>';
echo '</tr>';
}
echo '</tbody>';
echo '</table>';
if ($total_rows > $rows_per_page) {
echo '<p><a class="btn" href="?q=' . urlencode($q) . '&bookmark=' . $bookmark . '">More »</a></p>';
}
}
echo '</div>
</body>
</html>';
}
function DisplayHtmlContent()
{
global $config;
echo html_page_header(true, '', 'name');
echo '<h1>' . $this->GetTitle() . '</h1>';
echo '<h2>Identifiers</h2>';
echo '<ul>';
if ($this->object->NameBankID != 0) {
echo '<li>' . 'urn:lsid:ubio.org:namebank:' . $this->object->NameBankID . '</li>';
}
echo '</ul>';
// Taxon name (nomenclators)
$acts = acts_for_namestring($this->GetTitle());
$act_refs = references_for_acts_for_namestring($this->GetTitle());
if (count($acts) > 0) {
echo '<h2>Taxonomic names</h2>';
echo '<ul>';
foreach ($acts as $tn) {
echo '<li>' . $tn->global_id . '</li>';
}
echo '</ul>';
}
$col = col_accepted_name_for($this->GetTitle());
if (isset($col->name)) {
echo '<h2>Catalogue of Life accepted name</h2>' . "\n";
echo '<p>';
echo '<span><a href="' . $config['web_root'] . 'name/' . $col->name . '">' . $col->name . '</a>' . ' ' . $col->author . '</span>';
echo '</p>' . "\n";
// Synonyms
$col_synonyms = col_synonyms_for_namecode($col->name_code);
if (count($col_synonyms) != 0) {
echo '<h3>Synonyms</h3>' . "\n";
echo '<ul>' . "\n";
foreach ($col_synonyms as $s) {
echo '<li><a href="' . $config['web_root'] . 'name/' . $s->name . '">' . $s->name . '</a> ' . $s->author . '</li>' . "\n";
}
echo '</ul>' . "\n";
}
}
if (1) {
/*
// What pages have this name? (BHL timeline)
$hits = bhl_name_search($this->object->NameBankID);
if (count($hits) > 0)
{
echo '<h2>BHL</h2>' . "\n";
echo '<h3>Distribution of name in BHL</h3>';
echo '<div>' . "\n";
echo ' <img src="' . sparkline_bhl_name($hits, 360,100) . '" alt="sparkline" />' . "\n";
echo '</div>' . "\n";
}
else
{
//echo '<p>Name not found in BHL</p>';
}
*/
// What articles have this name?
echo '<hr />';
echo '<h2>References in BioStor</h2>';
// echo '<p><img src="/images/star.png"> indicates reference that publishes a "nomenclatural act", such as publishing the name.</p>';
echo '<div>';
echo '<div style="display:inline;border:1px solid rgb(192,192,192);background-color:#D8F3C9;width:20px;height:20px;"> </div>';
echo ' Reference contains nomenclatural act, such as publishing the name';
echo '</div>';
echo '<p />';
// Find using BHL bhl_page_name index
//$refs = bhl_references_with_name($this->object->NameBankID);
$refs = bhl_references_with_namestring($this->GetTitle());
// Merge with references from nomenclators
$refs = array_merge($refs, $act_refs);
$refs = array_unique($refs);
//print_r($refs);
if (count($refs) == 0) {
echo '<p>[No references]</p>';
}
/*
echo '<ul class="reference-list">';
foreach($refs as $reference_id)
{
$reference = db_retrieve_reference ($reference_id);
echo '<li ';
if (in_array($reference_id, $act_refs))
{
echo 'class="act"';
}
else
{
echo 'class="default"';
}
echo '>';
echo '<a href="' . $config['web_root'] . 'reference/' . $reference_id . '">' . $reference->title . '</a><br/>';
echo '<span style="color:green;">' . reference_authors_to_text_string($reference);
if (isset($reference->year))
{
echo ' (' . $reference->year . ')';
}
echo ' ' . reference_to_citation_text_string($reference) . '</span>';
echo ' ' . reference_to_coins($reference);
if (0)
{
echo '<div>';
echo bhl_pages_with_name_thumbnails($reference_id,$this->object->NameBankID);
echo '</div>';
}
echo '</li>';
}
echo '</ul>';
*/
echo '<table cellspacing="0" cellpadding="2" width="100%">';
foreach ($refs as $reference_id) {
$reference = db_retrieve_reference($reference_id);
echo '<tr';
if (in_array($reference_id, $act_refs)) {
echo ' style="background-color:#D8F3C9;"';
}
echo '>';
if ($reference->PageID != 0) {
$image = bhl_fetch_page_image($reference->PageID);
$imageURL = $image->thumbnail->url;
} else {
// if it's an article we could use journal image
$imageURL = 'http://bioguid.info/issn/image.php?issn=' . $reference->issn;
}
echo '<td valign="top"><img style="border:1px solid rgb(192,192,192);" src="' . $imageURL . '" width="40" />';
echo '</td>';
echo '<td valign="top">';
echo '<a href="' . $config['web_root'] . 'reference/' . $reference_id . '">' . $reference->title . '</a><br/>';
echo '<span>' . reference_authors_to_text_string($reference);
if (isset($reference->year)) {
echo ' (' . $reference->year . ')';
}
echo ' ' . reference_to_citation_text_string($reference) . '</span>';
echo ' ' . reference_to_coins($reference);
if (0) {
echo '<div>';
echo bhl_pages_with_name_thumbnails($reference_id, $this->object->NameBankID);
echo '</div>';
}
echo '</td>';
echo '</tr>';
}
echo '</table>';
/*
$refs = col_references_for_name($this->GetTitle());
if (count($refs) != 0)
{
echo '<h2>Catalogue of Life Bibliography</h2>';
echo '<ol>';
foreach($refs as $ref)
{
echo '<li style="border-bottom:1px dotted rgb(128,128,128);padding:4px;">';
echo '<span>';
echo '[' . $ref->record_id . '] ';
if (isset($ref->reference_type))
{
echo '[' . $ref->reference_type . '] ';
}
echo $ref->author;
echo ' ';
echo $ref->year;
echo ' ';
echo $ref->title;
echo '. ';
echo $ref->source;
echo '</span>';
echo '</li>';
}
echo '</ol>';
}
*/
}
}
function DisplayHtmlContent()
{
global $config;
log_access($this->id, 'html');
echo html_page_header(true, '', 'name');
// Embed first page of OCR text, added 2011-12-07
if ($this->in_bhl) {
$pages = bhl_retrieve_reference_pages($this->id);
$page_ids = array($pages[0]->PageID);
$text = bhl_fetch_text_for_pages($page_ids);
$text = str_replace('\\n', '', $text);
$text = str_replace('- ', '-', $text);
$text = str_replace('- ', '-', $text);
echo "\n<!-- First page of OCR text -->\n";
echo '<div style="display:none;">' . "\n";
echo htmlentities($text, ENT_COMPAT, "UTF-8");
echo '</div>' . "\n";
}
echo '<div style="float:right;background-color:rgb(230,242,250);padding:6px">' . "\n";
echo '<h2>Identifiers</h2>' . "\n";
echo '<ul class="guid-list">' . "\n";
echo '<li class="permalink">' . '<div itemscope itemtype="http://schema.org/ScholarlyArticle">' . '<a href="' . $config['web_root'] . 'reference/' . $this->id . '" title="Permalink">' . $config['web_root'] . 'reference/' . $this->id . '</a>' . '</div>' . '</li>' . "\n";
if ($this->in_bhl) {
echo '<li class="bhl"><a href="http://www.biodiversitylibrary.org/page/' . $this->object->PageID . '" target="_new" title="BHL page" onClick="_gaq.push([\'_trackEvent\', \'Outbound Links\', \'bhl\', \'' . $this->object->PageID . '\', 0]);">' . $this->object->PageID . '</a></li>' . "\n";
}
if (isset($this->object->doi)) {
echo '<li class="doi"><a href="http://dx.doi.org/' . $this->object->doi . '" target="_new" title="DOI" onClick="_gaq.push([\'_trackEvent\', \'Outbound Links\', \'doi\', \'' . $this->object->doi . '\', 0]);">' . $this->object->doi . '</a></li>' . "\n";
}
if (isset($this->object->url)) {
echo '<li class="url"><a href="' . $this->object->url . '" target="_new" title="URL">' . trim_string($this->object->url, 30) . '</a></li>' . "\n";
}
if (isset($this->object->pdf)) {
echo '<li class="pdf"><a href="' . $this->object->pdf . '" target="_new" title="PDF">' . trim_string($this->object->pdf, 30) . '</a></li>' . "\n";
}
if (isset($this->object->hdl)) {
echo '<li class="handle"><a href="http://hdl.handle.net/' . $this->object->hdl . '" target="_new" title="Handle">' . $this->object->hdl . '</a></li>' . "\n";
}
if (isset($this->object->lsid)) {
echo '<li class="lsid"><a href="' . $config['web_root'] . $this->object->lsid . '" title="LSID">' . $this->object->lsid . '</a></li>' . "\n";
}
if (isset($this->object->pmid)) {
echo '<li class="pmid"><a href="http://www.ncbi.nlm.nih.gov/pubmed/' . $this->object->pmid . '" target="_new" title="PMID" >' . $this->object->pmid . '</a></li>' . "\n";
}
echo '</ul>' . "\n";
echo '<h2>Export</h2>' . "\n";
echo '<ul class="export-list">' . "\n";
// Mendeley
echo '<li class="mendeley"><a href="http://www.mendeley.com/import/?url=' . urlencode($config['web_root'] . 'reference/' . $this->id) . '" title="Add to Mendeley" target="_new" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'Mendeley\', \'' . $this->id . '\', 0]);">Mendeley</a></li>';
if ($this->in_bhl) {
echo '<li class="pdf"><a href="' . $config['web_root'] . 'reference/' . $this->id . '.pdf" title="PDF" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'pdf\', \'' . $this->id . '\', 0]);">PDF</a></li>';
}
echo '<li class="xml"><a href="' . $config['web_root'] . 'reference/' . $this->id . '.xml" title="Endnote XML" target="_new" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'Endnote\', \'' . $this->id . '\', 0]);">Endnote XML</a></li>';
echo '<li class="ris"><a href="' . $config['web_root'] . 'reference/' . $this->id . '.ris" title="RIS" target="_new" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'RIS\', \'' . $this->id . '\', 0]);">Reference manager</a></li>';
echo '<li class="bibtex"><a href="' . $config['web_root'] . 'reference/' . $this->id . '.bib" title="BibTex" target="_new" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'bibtex\', \'' . $this->id . '\', 0]);">BibTex</a></li>';
echo '<li class="bibjson"><a href="' . $config['web_root'] . 'reference/' . $this->id . '.bibjson" title="BibJSON" target="_new" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'bibjson\', \'' . $this->id . '\', 0]);">BibJSON</a></li>';
echo '<li class="wikipedia"><a href="' . $config['web_root'] . 'reference/' . $this->id . '.wikipedia" title="Wikipedia" target="_new" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'Wikipedia\', \'' . $this->id . '\', 0]);">Wikipedia</a></li>';
if ($this->in_bhl) {
echo '<li class="text"><a href="' . $config['web_root'] . 'reference/' . $this->id . '.text" title="Text" onClick="_gaq.push([\'_trackEvent\', \'Export\', \'text\', \'' . $this->id . '\', 0]);">Text</a></li>';
}
echo '</ul>' . "\n";
echo '</div>' . "\n";
//------------------------------------------------------------------------------------------
echo '<div itemscope itemtype="http://schema.org/ScholarlyArticle">';
echo '<h1>' . '<div itemprop="name">' . $this->GetTitle() . '</div>' . '</h1>' . "\n";
//------------------------------------------------------------------------------------------
// Authors
echo '<div>' . "\n";
$count = 0;
$num_authors = count($this->object->authors);
if ($num_authors > 0) {
foreach ($this->object->authors as $author) {
echo '<a href="' . $config['web_root'] . 'author/' . $author->id . '">';
echo $author->forename . ' ' . $author->lastname;
if (isset($author->suffix)) {
echo ' ' . $author->suffix;
}
echo '</a>';
$count++;
if ($count < $num_authors - 1) {
echo ', ';
} else {
if ($count < $num_authors) {
echo ' and ';
}
}
}
}
echo "\n" . '</div>' . "\n";
//------------------------------------------------------------------------------------------
// Metadata and COinS
echo '<div>' . "\n";
echo '<div itemprop="description">';
echo '<span class="journal">';
// Various options for linking journal.
if (isset($this->object->issn)) {
echo '<a href="' . $config['web_root'] . 'issn/' . $this->object->issn . '">';
echo $this->object->secondary_title;
echo '</a>';
} elseif (isset($this->object->oclc)) {
echo '<a href="' . $config['web_root'] . 'oclc/' . $this->object->oclc . '">';
echo $this->object->secondary_title;
echo '</a>';
} else {
echo $this->object->secondary_title;
}
echo '</span>';
echo ' ';
if (isset($this->object->series)) {
echo ' <span class="volume">(' . $this->object->series . ') </span>';
}
echo '<span class="volume">' . $this->object->volume . '</span>';
if (isset($this->object->issue)) {
echo '<span class="issue">' . '(' . $this->object->issue . ')' . '</span>';
}
echo ':';
echo ' ';
echo '<span class="pages">' . $this->object->spage . '</span>';
if (isset($this->object->epage)) {
echo '<span class="pages">' . '-' . $this->object->epage . '</span>';
}
if (isset($this->object->year)) {
echo ' ';
echo '<span class="year">' . '(' . $this->object->year . ')' . '</span>';
}
echo reference_to_coins($this->object);
echo '</div>' . "\n";
echo '</div>' . "\n";
echo '</div>';
// schema
//------------------------------------------------------------------------------------------
// When record added and updated
echo '<p class="explanation">Reference added ';
echo distanceOfTimeInWords(strtotime($this->object->created), time(), true);
echo ' ago';
echo '</p>' . "\n";
//------------------------------------------------------------------------------------------
// Social bookmarking
// echo '<g:plusone size="tall"></g:plusone>';
echo '<a href="http://twitter.com/share" class="twitter-share-button" data-count="vertical" data-via="rdmpage" data-related="biostor_org">Tweet</a><script type="text/javascript" src="http://platform.twitter.com/widgets.js"></script>';
//------------------------------------------------------------------------------------------
// Export options
/* echo '<h2>Export</h2>' . "\n";
echo '<div>' . "\n";
echo '<span><a href="' . $config['web_root'] . 'reference/' . $this->id . '.xml" title="Endnote XML">Endnote XML</a></span>';
echo ' | ';
echo '<span><a href="' . $config['web_root'] . 'reference/' . $this->id . '.ris" title="RIS">Reference manager</a></span>';
echo ' | ';
echo '<span><a href="' . $config['web_root'] . 'reference/' . $this->id . '.bib" title="BibTex">BibTex</a></span>';
if ($this->in_bhl)
{
echo ' | ';
echo '<span><a href="' . $config['web_root'] . 'reference/' . $this->id . '.text" title="Text">Text</a></span>';
}
echo '</div>' . "\n";
*/
//------------------------------------------------------------------------------------------
// Identifiers
/* echo '<h2>Identifiers</h2>' . "\n";
echo '<ul>' . "\n";
if ($this->in_bhl)
{
// BHL reference
echo '<li><a href="http://www.biodiversitylibrary.org/page/' . $this->object->PageID . '" target="_new">BHL PageID:' . $this->object->PageID . '</a></li>' . "\n";
}
if (isset($this->object->sici))
{
echo '<li><a href="' . $config['web_root'] . 'sici/' . $this->object->sici . '">' . $this->object->sici . '</a></li>' . "\n";
}
if (isset($this->object->url))
{
echo '<li><a href="' . $this->object->url . '" target="_new">' . $this->object->url . '</a></li>' . "\n";
}
if (isset($this->object->pdf))
{
echo '<li><a href="' . $this->object->pdf . '" target="_new">' . $this->object->pdf . '</a></li>' . "\n";
}
if (isset($this->object->doi))
{
echo '<li><a href="http://dx.doi.org/' . $this->object->doi . '" target="_new">' . $this->object->doi . '</a></li>' . "\n";
}
if (isset($this->object->hdl))
{
echo '<li><a href="http://hdl.handle.net/' . $this->object->hdl . '" target="_new">' . $this->object->hdl . '</a></li>' . "\n";
}
if (isset($this->object->lsid))
{
echo '<li><a href="' . $config['web_root'] . $this->object->lsid . '">' . $this->object->lsid . '</a></li>' . "\n";
}
if (isset($this->object->pmid))
{
echo '<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/' . $this->object->pmid . '" target="_new">' . $this->object->pmid . '</a></li>' . "\n";
}
echo '</ul>' . "\n";*/
//------------------------------------------------------------------------------------------
// Linking
/*
echo '<div>' . "\n";
echo '<span><a href="' . $config['web_root'] . 'reference/' . $this->id . '/backlinks" title="References">Cites (' . num_cites($this->id) . ')</a></span>';
echo ' | ';
echo '<span><a href="' . $config['web_root'] . 'reference/' . $this->id . '/forwardlinks" title="Forward links">Cited by (' . num_cited_by($this->id) . ')</a></span>';
echo '</div>' . "\n";
*/
//------------------------------------------------------------------------------------------
if ($this->in_bhl) {
//--------------------------------------------------------------------------------------
echo '<h2>Viewer</h2>';
echo '<p id="viewer_status"></p>' . "\n";
echo '<table width="100%" >';
echo '<tr valign="top"><td>';
echo bhl_reference_viewer($this->id, $this->page);
echo '</td>';
echo '<td>';
echo $this->DisplayEditForm();
echo '</td></tr>';
echo '</table>';
if (0) {
//--------------------------------------------------------------------------------------
$tag_cloud = name_tag_cloud($this->taxon_names);
if ($tag_cloud != '') {
echo '<h2>Taxon name tag cloud</h2>';
echo '<p class="explanation">Taxonomic names extracted from OCR text for document using uBio tools.</p>';
echo $tag_cloud;
echo '<h2>Taxonomic classification</h2>';
if ($config['use_gbif']) {
echo '<p class="explanation">GBIF classification for taxonomic names in document</p>';
} else {
echo '<p class="explanation">Catalogue of Life classification for taxonomic names in document</p>';
}
echo '<div id="taxon_names"></div>';
echo '<script type="text/javascript">make_tag_tree();</script>';
}
}
//--------------------------------------------------------------------------------------
if (count($this->localities) != 0) {
echo '<h2>Localities</h2>';
echo '<p class="explanation">Localities extracted from OCR text.</p>';
echo '<div id="map_canvas" style="width: 600px; height: 300px"></div>';
}
//--------------------------------------------------------------------------------------
if (count($this->specimens) != 0) {
echo '<h2>Specimens</h2>';
echo '<p class="explanation">Specimen codes extracted from OCR text.</p>';
echo '<ul style="-moz-column-width: 13em; -webkit-column-width: 13em; -moz-column-gap: 1em; -webkit-column-gap: 1em;">';
foreach ($this->specimens as $occurrence) {
echo '<li';
if (isset($occurrence->occurrenceID)) {
//echo $occurrence->occurrenceID;
echo ' class="gbif"';
} else {
echo ' class="blank"';
}
echo '>';
echo '<a href="specimen/' . rawurlencode($occurrence->code) . '">' . $occurrence->code . '</a>';
echo '</li>';
}
echo '</ul>';
}
} else {
echo '<table width="100%" >';
echo '<tr><td valign="top" width="600">';
$have_content = false;
// PDF displayed using Google Docs
if (!$have_content) {
// If we have a PDF display it using Google Docs Viewer http://docs.google.com/viewer
if ($this->object->url) {
if (preg_match('/\\.pdf$/', $this->object->url)) {
echo '<iframe src="http://docs.google.com/viewer?url=';
echo urlencode($this->object->url) . '&embedded=true" width="600" height="700" style="border: none;">' . "\n";
echo '</iframe>' . "\n";
$have_content = true;
}
}
}
if (!$have_content) {
if (isset($this->object->abstract)) {
echo '<h3>Abstract</h3>' . "\n";
echo '<div>' . $this->object->abstract . '</div>' . "\n";
$have_content = true;
}
}
if (!$have_content) {
echo '<span>[No text or abstract to display]</span>';
}
echo '</td>';
echo '<td>';
echo $this->DisplayEditForm();
echo '</td></tr>';
echo '</table>';
}
/*
//------------------------------------------------------------------------------------------
// Nomenclature (experimental)
$acts = acts_in_publication($this->id);
if (count($acts) > 0)
{
echo '<h2>Names published</h2>' . "\n";
echo '<p class="explanation">New names or combinations published in this reference.</p>' . "\n";
echo '<table cellspacing="0" cellpadding="2">' . "\n";
echo '<tr><th>Name</th><th>Identifier</th></tr>' . "\n";
foreach ($acts as $tn)
{
echo '<tr>';
echo '<td style="border-bottom:1px solid rgb(228,228,228);"><a href="' . $config['web_root'] . 'name/' . urlencode($tn->ToHTML()) . '">' . $tn->ToHTML() . '</td>';
echo '<td style="border-bottom:1px solid rgb(228,228,228);">' . $tn->global_id . '</td>';
echo '</tr>' . "\n";
}
echo '</table>' . "\n";
}
*/
}
function display_publication($publication)
{
global $couch;
global $config;
echo html_html_open();
echo html_head_open();
echo html_title($publication->title . ' - ' . $config['site_name']);
echo html_include_css('css/main.css');
echo html_include_css('css/viewer.css');
echo html_include_script('js/jquery-1.4.4.min.js');
echo html_include_script('js/viewer.js');
echo html_head_close();
echo html_body_open();
if (1) {
echo '<div style="position:relative;">';
// Metadata
echo '<div style="position:absolute;top:0px;left:620px;padding:10px;">';
echo '<div><span><a href="' . $config['web_root'] . '">' . $config['site_name'] . '</a></span></div>';
echo '<p></p>';
echo '<span style="font-weight:bold;font-size:18px;">' . $publication->title . '</span>';
echo '<div>' . 'by ' . reference_authors_to_text_string($publication->authors, false, true) . '</div>';
$outlet = $publication->publication_outlet;
// This ensures we double urlencode "&"
$outlet = str_replace("&", urlencode("&"), $outlet);
echo '<div>' . '<a href="' . $config['web_root'] . 'publication_outlet/' . urlencode($outlet) . '">' . '<i>' . $publication->publication_outlet . '</i>' . '</a>' . ' ' . $publication->volume . ':' . $publication->pages . ' (' . $publication->year . ')' . '</div>';
// External links ---------------------------------------------------------------------------------------
echo '<div>';
echo '<ul>';
if ($publication->_id) {
echo '<li><a href="http://lsid.tdwg.org/summary/urn:lsid:biodiversity.org.au:afd.publication:' . $publication->_id . '" target="_new">urn:lsid:biodiversity.org.au:afd.publication:' . $publication->_id . '</li>';
}
if (isset($publication->identifiers)) {
if (isset($publication->identifiers->doi)) {
echo '<li>' . '<a href="http://dx.doi.org/' . $publication->identifiers->doi . '" target="_new">doi:' . $publication->identifiers->doi . '</a></li>';
}
if (isset($publication->identifiers->hdl)) {
echo '<li>' . '<a href="http://hdl.handle.net/' . $publication->identifiers->hdl . '" target="_new">hdl:' . $publication->identifiers->hdl . '</a></li>';
}
if (isset($publication->identifiers->biostor)) {
echo '<li>' . '<a href="http://biostor.org/reference/' . $publication->identifiers->biostor . '" target="_new">BioStor</a></li>';
}
if (isset($publication->pageIdentifiers)) {
echo '<li>' . '<a href="http://biodiversitylibrary.org/page/' . $publication->pageIdentifiers[0] . '" target="_new">BHL</a></li>';
}
}
if (isset($publication->urls)) {
foreach ($publication->urls as $url) {
if (preg_match('/http:\\/\\/ci.nii.ac.jp\\/naid\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
if (preg_match('/http:\\/\\/gallica.bnf.fr\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
if (preg_match('/http:\\/\\/www.jstor.org\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
}
}
echo '</div>';
echo reference_to_coins($publication);
echo '<div><a href="http://biostor.org/openurlhook.php?' . reference_to_openurl($publication) . '&webhook=' . urlencode($config['web_server'] . $config['web_root'] . 'webhook.php') . '" target="_new">OpenURL Hook</a></div>';
//------------------------------------------------------------------------------------------
// Names
$resp = $couch->send("GET", "/" . $config['couchdb'] . "/_design/publication/_view/taxonNames?key=" . urlencode('"' . $publication->_id . '"'));
$names = json_decode($resp);
if (count($names->rows) > 0) {
echo '<h3>Names published</h3>';
echo '<ul>';
foreach ($names->rows as $row) {
echo '<li>' . '<a href="id/' . $row->value->_id . '">' . $row->value->taxonName . '</a></li>';
}
echo '</ul>';
}
echo '</div>';
// --- end metadata
// Viewer
echo '<div style="position:absolute;top:0px;left:0px;width:600px;">';
$has_fulltext = isset($publication->identifiers->biostor) || isset($publication->pdf);
if (!$has_fulltext) {
if (isset($publication->identifiers->doi)) {
$url = 'http://dx.doi.org/' . $publication->identifiers->doi;
echo '<div style="width:600px;height:800px;border:1px solid rgb(192,192,192);">';
echo '<iframe src="' . $url . '" width="600" height="800" style="border: none;">';
echo '</iframe>';
echo '</div>';
} else {
if (count($publication->urls) > 0) {
$display_url = '';
foreach ($publication->urls as $url) {
if (preg_match('/http:\\/\\/ci.nii.ac.jp\\/naid\\//', $url)) {
$display_url = $url;
break;
}
if (preg_match('/http:\\/\\/gallica.bnf.fr\\//', $url)) {
$display_url = $url;
break;
}
if (preg_match('/http:\\/\\/www.jstor.org\\//', $url)) {
$display_url = $url;
break;
}
}
if ($display_url != '') {
echo '<div style="width:600px;height:800px;border:1px solid rgb(192,192,192);">';
echo '<iframe src="' . $display_url . '" width="600" height="800" style="border: none;">';
echo '</iframe>';
echo '</div>';
}
} else {
echo '<div style="width:600px;height:800px;border:1px solid rgb(192,192,192);">
<div style="position:absolute;top:300px;left:0px;width:600px;color:rgb(192,192,192);text-align:center;font-size:72px;">No content</div>
</div>';
}
}
} else {
// PDF
if (isset($publication->pdf)) {
echo '<div>';
echo '<iframe src="http://docs.google.com/viewer?url=';
echo str_replace(' ', '%20', $publication->pdf) . '&embedded=true" width="600" height="800" style="border: none;">';
echo '</iframe>';
echo '</div>';
} else {
// BioStor
if (isset($publication->identifiers->biostor)) {
echo '<script> pages=[' . join(",", $publication->pageIdentifiers) . ']; </script>';
echo '
<div style="position:relative;width:600px;height:800px;">
<div id="header" >
<div style="float:right;padding:8px;margin-right:10px;">
<span id="page_counter">1/?</span>
<span> </span>
<span> </span>
<img id="previous_page" src="images/previous.png" border="0" onclick="previous();" title="Show previous page">
<span> </span>
<img id="next_page" src="images/next.png" border="0" onclick="next();" title="Show next page">
<span> </span>
<span> </span>
<span> </span>
<img src="images/fourpages.png" border="0" onclick="show_all_pages();" title="Show all pages">
<span> </span>
<img src="images/onepage.png" border="0" onclick="show_page(-1);" title="Fit page to viewer">
</div>
</div>
<div id="page_container">
<img id="page_image" />
<div id="all_pages" ></div>
</div>
</div>
<script>
show_page(0);
</script>';
}
}
}
echo '</div>
</div>';
} else {
//----------------------------------------------------------------------------------------------
// Home
echo '<span><a href="' . $config['web_root'] . '">' . $config['site_name'] . '</a></span>';
echo html_search_box();
//----------------------------------------------------------------------------------------------
// Object
echo '<div>';
echo '<h1>' . $publication->title . '</h1>';
echo '<div>' . 'by ' . reference_authors_to_text_string($publication->authors, false, true) . '</div>';
echo '<div>' . '<i>' . $publication->publication_outlet . '</i>' . ' ' . $publication->volume . ':' . $publication->pages . ' (' . $publication->year . ')' . '</div>';
//echo '<div>' . $publication->_id . '</div>';
/*
if (isset($publication->abstract))
{
echo '<div>' . $publication->abstract . '</div>';
}
*/
// External links
echo '<ul>';
if (isset($publication->identifiers)) {
if (isset($publication->identifiers->doi)) {
echo '<li>' . '<a href="http://dx.doi.org/' . $publication->identifiers->doi . '" target="_new">doi:' . $publication->identifiers->doi . '</a></li>';
}
if (isset($publication->identifiers->hdl)) {
echo '<li>' . '<a href="http://hdl.handle.net/' . $publication->identifiers->hdl . '" target="_new">hdl:' . $publication->identifiers->hdl . '</a></li>';
}
if (isset($publication->identifiers->biostor)) {
echo '<li>' . '<a href="http://biostor.org/reference/' . $publication->identifiers->biostor . '" target="_new">BioStor</a></li>';
}
if (isset($publication->pageIdentifiers)) {
echo '<li>' . '<a href="http://biodiversitylibrary.org/page/' . $publication->pageIdentifiers[0] . '" target="_new">BHL</a></li>';
}
}
if (isset($publication->urls)) {
foreach ($publication->urls as $url) {
if (preg_match('/http:\\/\\/ci.nii.ac.jp\\/naid\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
}
}
echo '</ul>';
echo '</div>';
//----------------------------------------------------------------------------------------------
// Names
$resp = $couch->send("GET", "/" . $config['couchdb'] . "/_design/publication/_view/taxonNames?key=" . urlencode('"' . $publication->_id . '"'));
$names = json_decode($resp);
if (count($names->rows) > 0) {
echo '<h2>Names published</h2>';
echo '<ul>';
foreach ($names->rows as $row) {
echo '<li>' . '<a href="id/' . $row->value->_id . '">' . $row->value->taxonName . '</a></li>';
}
echo '</ul>';
}
//----------------------------------------------------------------------------------------------
// Content
echo '<h2>Content</h2>';
$has_fulltext = isset($publication->identifiers->biostor) || isset($publication->pdf);
if (!$has_fulltext) {
if (isset($publication->identifiers->doi)) {
$url = 'http://dx.doi.org/' . $publication->identifiers->doi;
echo '<div>';
echo '<iframe src="' . $url . '" width="100%" height="700" style="border: none;">';
echo '</iframe>';
echo '</div>';
}
} else {
// PDF
if (isset($publication->pdf)) {
echo '<div>';
echo '<iframe src="http://docs.google.com/viewer?url=';
echo urlencode($publication->pdf) . '&embedded=true" width="700" height="700" style="border: none;">';
echo '</iframe>';
echo '</div>';
} else {
// BioStor
if (isset($publication->identifiers->biostor)) {
echo '<script> pages=[' . join(",", $publication->pageIdentifiers) . ']; </script>';
echo '
<div style="position:relative;width:700px;height:700px;">
<div id="header" >
<div style="float:right;padding:8px;margin-right:10px;">
<span id="page_counter">1/?</span>
<span> </span>
<span> </span>
<img id="previous_page" src="images/previous.png" border="0" onclick="previous();" title="Show previous page">
<span> </span>
<img id="next_page" src="images/next.png" border="0" onclick="next();" title="Show next page">
<span> </span>
<span> </span>
<span> </span>
<img src="images/fourpages.png" border="0" onclick="show_all_pages();" title="Show all pages">
<span> </span>
<img src="images/onepage.png" border="0" onclick="show_page(-1);" title="Fit page to viewer">
</div>
</div>
<div id="page_container">
<img id="page_image" />
<div id="all_pages" ></div>
</div>
</div>
<script>
show_page(0);
</script>';
}
}
}
}
echo html_body_close();
echo html_html_close();
}
$image = bhl_fetch_page_image($reference->PageID);
$imageURL = $image->thumbnail->url;
} else {
// if it's an article we could use journal image
$imageURL = 'http://bioguid.info/issn/image.php?issn=' . $reference->issn;
}
echo '<td valign="top"><img style="border:1px solid rgb(192,192,192);" src="' . $imageURL . '" width="40" />';
echo '</td>';
echo '<td valign="top">';
echo '<a href="' . $config['web_root'] . 'reference/' . $reference_id . '">' . $reference->title . '</a><br/>';
echo '<span>' . reference_authors_to_text_string($reference);
if (isset($reference->year)) {
echo ' (' . $reference->year . ')';
}
echo ' ' . reference_to_citation_text_string($reference) . '</span>';
echo ' ' . reference_to_coins($reference);
if (0) {
echo '<div>';
echo bhl_pages_with_name_thumbnails($reference_id, $this->object->NameBankID);
echo '</div>';
}
echo '</td>';
echo '</tr>';
}
echo '</table>';
echo html_body_close(true);
// true to show Disqus comments
echo html_html_close();
?>
