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";
}
$c[] = $co->id;
}
$journal_names = array();
foreach ($refs as $reference_id) {
global $config;
$reference = db_retrieve_reference($reference_id);
$item = new stdclass();
$item->uri = $config['web_root'] . 'reference/' . $reference_id;
$item->type = $reference->genre;
$item->label = $reference->title;
// Group journals
if (!isset($journal_names[$reference->issn])) {
$journal_names[$reference->issn] = $reference->secondary_title;
}
$item->journal = $journal_names[$reference->issn];
$item->citation = reference_authors_to_text_string($reference) . ' (' . $reference->year . ') ' . reference_to_citation_text_string($reference);
$item->year = $reference->year;
if ($reference->PageID != 0) {
$image = bhl_fetch_page_image($reference->PageID);
$item->imageURL = $image->thumbnail->url;
} else {
// if it's an article we could use journal image
$item->imageURL = 'http://bioguid.info/issn/image.php?issn=' . $reference->issn;
}
$item->coauthors = array();
foreach ($reference->authors as $author) {
if (in_array($author->id, $c)) {
$item->coauthors[] = $author->forename . ' ' . $author->lastname;
}
}
$exhibit->items[] = $item;
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($reference);
}
}
echo '</ul>';
echo '</li>';
}
echo '</ul>';
}
}
function reference_to_solr($reference)
{
$obj = reference_to_mendeley($reference);
$item = array();
$item['id'] = 'reference/' . $reference->reference_id;
$item['title'] = $obj->title;
$item['publication_outlet'] = $obj->publication_outlet;
$item['year'] = $obj->year;
$authors = array();
foreach ($obj->authors as $a) {
$authors[] = $a->forename . ' ' . $a->surname;
}
$item['authors'] = $authors;
$item['citation'] = reference_authors_to_text_string($reference) . ' ' . $reference->year . ' ' . $reference->title . ' ' . reference_to_citation_text_string($reference);
return $item;
}
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>';
}
}
}
<?php
require_once '../db.php';
require_once '../bhl_text.php';
require_once '../reference.php';
$id = $_GET['id'];
$callback = '';
if (isset($_GET['callback'])) {
$callback = $_GET['callback'];
}
$reference = db_retrieve_reference($id);
$obj = new stdclass();
$obj->title = $reference->title;
$obj->description = '<b>' . $reference->title . '</b>' . "<br/>" . 'by ' . reference_authors_to_text_string($reference) . "<br/>" . reference_to_citation_text_string($reference);
$obj->id = $id;
$obj->canonical_url = $config['web_root'] . 'reference/' . $id;
$bhl_pages = bhl_retrieve_reference_pages($id);
$obj->pages = count($bhl_pages);
$obj->resources = new stdclass();
$obj->resources->page = new stdclass();
$obj->resources->page->text = 'http://biostor.org/reference/' . $id . '/pages/{page}';
$obj->resources->page->image = 'http://biostor.org/reference/' . $id . '/pages/{page}-{size}';
$obj->resources->search = 'http://biostor.org/dvs/' . $id . '/json?q={query}';
$obj->sections = array();
$obj->annotations = array();
// support text indexing
$sql = 'SELECT * FROM rdmp_documentcloud WHERE reference_id=' . $id . ' LIMIT 1';
//echo $sql;
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
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 $ref->source;
echo '</span>';
echo '</li>';
}
echo '</ol>';
}
*/
}
}
function display_publication($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(",", $publication->pageIdentifiers) . ']; </script>';
echo '
<div style="position:relative;width:700px;height:700px;">
<div id="header" >
<div style="float:right;padding:8px;margin-right:10px;">
<span id="page_counter">1/?</span>
<span> </span>
<span> </span>
<img id="previous_page" src="images/previous.png" border="0" onclick="previous();" title="Show previous page">
<span> </span>
<img id="next_page" src="images/next.png" border="0" onclick="next();" title="Show next page">
<span> </span>
<span> </span>
<span> </span>
<img src="images/fourpages.png" border="0" onclick="show_all_pages();" title="Show all pages">
<span> </span>
<img src="images/onepage.png" border="0" onclick="show_page(-1);" title="Fit page to viewer">
</div>
</div>
<div id="page_container">
<img id="page_image" />
<div id="all_pages" ></div>
</div>
</div>
<script>
show_page(0);
</script>';
}
}
}
}
echo html_body_close();
echo html_html_close();
}
/**
* @brief Create PDF for a reference
*
* We create a simple cover page for the PDF. This page contains basic bibliographic metadata
* for the PDF, in order for Mendeley to process the PDF correctly. In response to my discovery
* that Mendeley doesn't accept all XMP (Ticket#2010040110000015) support@mendeley.com replied that
* they have some heuristic tests to see if the metadata is valid, such as whether the information
* about the title and authors occurs on the first of the PDF.
*
*
* @param reference_id Reference id
* @param pdf_filename Full path of PDF file to create
*
*/
function pdf_create($reference_id, $pdf_filename)
{
global $config;
// Get reference
$reference = db_retrieve_reference($reference_id);
// Get tags
$tags = pdf_tags($reference->reference_id, 10);
// Paper size
// A4 = 210 x 297
$paper_width = 210;
// mm
$paper_height = 297;
// mm
$margin = 10;
//----------------------------------------------------------------------------------------------
// PDF
$pdf = new FPDF('P', 'mm', 'A4');
//$pdf = PDF_Rotate('P', 'mm', 'A4');
//----------------------------------------------------------------------------------------------
// Basic metadata (e.g., that displayed by Mac OS X Preview)
$pdf->SetTitle($reference->title, true);
// true means use UTF-8
$pdf->SetAuthor(reference_authors_to_text_string($reference), true);
// true means use UTF-8
if (count($tags) > 0) {
$pdf->SetKeywords(join(", ", $tags), true);
}
//----------------------------------------------------------------------------------------------
// Cover page (partly to ensure Mendeley accepts XMP metadata)
$pdf->AddPage();
// Title
$pdf->SetFont('Arial', '', 24);
$pdf->SetXY($margin, $margin);
$pdf->Write(10, utf8_decode($reference->title));
// Authors
$y = $pdf->GetY();
$pdf->SetXY($margin, $y + 16);
$pdf->SetFont('Arial', 'B', 16);
$pdf->Write(6, utf8_decode(reference_authors_to_text_string($reference)));
// Citation
$y = $pdf->GetY();
$pdf->SetXY($margin, $y + 10);
$pdf->SetFont('Arial', 'I', 12);
$pdf->Write(6, utf8_decode($reference->secondary_title));
$pdf->SetFont('Arial', '', 12);
$pdf->Write(6, ' ' . $reference->volume);
if (isset($reference->issue)) {
$pdf->Write(6, '(' . $reference->issue . ')');
}
$pdf->Write(6, ':' . $reference->spage);
if (isset($reference->epage)) {
$pdf->Write(6, '-' . $reference->epage);
}
$pdf->Write(6, ' (' . $reference->year . ')');
// URL
$url = $config['web_root'] . 'reference/' . $reference->reference_id;
$pdf->Write(6, ' ');
$pdf->SetTextColor(0, 0, 255);
$pdf->SetFont('', 'U');
$pdf->Write(6, $url, $url);
$pdf->SetFont('', '');
$pdf->SetTextColor(0, 0, 0);
//----------------------------------------------------------------------------------------------
// If we add taxon names as keywords
if (count($tags) > 0) {
$keywords = "Keywords: " . join("; ", $tags);
$y = $pdf->GetY();
$pdf->SetXY($margin, $y + 10);
$pdf->Write(6, $keywords);
}
//----------------------------------------------------------------------------------------------
// Footer giving credit to BHL
$y = $paper_height;
$y -= $margin;
$y -= 40;
$pdf->Image($config['web_dir'] . '/images/cc/cc.png', 10, $y, 10);
$pdf->Image($config['web_dir'] . '/images/cc/by.png', 20, $y, 10);
$pdf->Image($config['web_dir'] . '/images/cc/nc.png', 30, $y, 10);
$pdf->SetXY(10, $y + 10);
$pdf->SetFont('Arial', '', 10);
$pdf->SetTextColor(0, 0, 0);
$pdf->Write(6, 'Page images from the Biodiversity Heritage Library, ');
//Then put a blue underlined link
$pdf->SetTextColor(0, 0, 255);
$pdf->SetFont('', 'U');
$pdf->Write(6, 'http://www.biodiversitylibrary.org/', 'http://www.biodiversitylibrary.org/');
$pdf->SetFont('', '');
$pdf->SetTextColor(0, 0, 0);
$pdf->Write(6, ', made available under a Creative Commons Attribution-Noncommercial License ');
$pdf->SetTextColor(0, 0, 255);
$pdf->SetFont('', 'U');
$pdf->Write(6, 'http://creativecommons.org/licenses/by-nc/2.5/', 'http://creativecommons.org/licenses/by-nc/2.5/');
//----------------------------------------------------------------------------------------------
// Add BHL page scans
$pages = bhl_retrieve_reference_pages($reference_id);
foreach ($pages as $page) {
$image = bhl_fetch_page_image($page->PageID);
$page_width = $paper_width;
$page_height = $paper_height;
$page_width -= 2 * $margin;
$page_height -= 2 * $margin;
// Fit to page
$img_height = $image->height;
$img_width = $image->width;
$w_scale = $page_width / $img_width;
$h_scale = $page_height / $img_height;
$scale = min($w_scale, $h_scale);
$img_height *= $scale;
$img_width *= $scale;
$pdf->AddPage();
$x_offset = ($paper_width - $img_width) / 2.0;
$y_offset = ($paper_height - $img_height) / 2.0;
$pdf->Image($image->file_name, $x_offset, $y_offset, $img_width);
}
$pdf->Output($pdf_filename, 'F');
pdf_add_xmp($reference, $pdf_filename, $tags);
}
if (in_array($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>';
echo html_body_close(true);
