function articles_for_item($ItemID)
{
global $db;
$obj = new stdclass();
$sql = 'SELECT * FROM bhl_title INNER JOIN bhl_item USING(TitleID) WHERE ItemID=' . $ItemID . ' LIMIT 1';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
if ($result->NumRows() == 1) {
$obj->ItemID = $result->fields['ItemID'];
$obj->FullTitle = $result->fields['FullTitle'];
$obj->VolumeInfo = $result->fields['VolumeInfo'];
} else {
}
if (isset($obj->ItemID)) {
$ids = array();
$sql = 'SELECT DISTINCT rdmp_reference.reference_id, page.SequenceOrder
FROM rdmp_reference_page_joiner
INNER JOIN page USING(PageID)
INNER JOIN rdmp_reference USING(PageID)
WHERE ItemID=' . $obj->ItemID . '
ORDER BY CAST(page.SequenceOrder AS SIGNED)';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
while (!$result->EOF) {
$ids[] = $result->fields['reference_id'];
$result->MoveNext();
}
$obj->articles = array();
foreach ($ids as $reference_id) {
$reference = db_retrieve_reference($reference_id);
if (isset($reference->oclc)) {
if ($reference->oclc == 0) {
unset($reference->oclc);
}
}
if (isset($reference->sici)) {
unset($reference->sici);
}
if (isset($reference->reference_cluster_id)) {
unset($reference->reference_cluster_id);
}
// get pages
$pages = bhl_retrieve_reference_pages($reference_id);
foreach ($pages as $page) {
$reference->bhl_pages[] = (int) $page->PageID;
}
$obj->articles[] = $reference;
}
}
//print_r($obj);
return $obj;
}
<?php
// geocode a reference
require_once dirname(__FILE__) . '/db.php';
require_once dirname(__FILE__) . '/lib.php';
require_once dirname(__FILE__) . '/geocoding.php';
require_once dirname(__FILE__) . '/bhl_text.php';
$ids = array(55225);
foreach ($ids as $reference_id) {
global $db;
echo $reference_id . "\n";
// remove any existing geocoding...
$pages = bhl_retrieve_reference_pages($reference_id);
foreach ($pages as $page) {
$sql = 'DELETE FROM rdmp_locality_page_joiner WHERE PageID=' . $page->PageID;
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
}
// redo
bhl_geocode_reference($reference_id);
}
function specimens_from_reference($reference_id)
{
global $db;
// delete any existing specimens
$sql = 'DELETE FROM rdmp_reference_specimen_joiner WHERE reference_id=' . $reference_id;
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
$pages = bhl_retrieve_reference_pages($reference_id);
$page_ids = array();
foreach ($pages as $p) {
$page_ids[] = $p->PageID;
}
//echo "PageIDs:\n";
//print_r($page_ids);
$text = bhl_fetch_text_for_pages($page_ids);
$text = str_replace('\\n', "\n", $text);
$text = str_replace("\n ", "\n", $text);
$specimens = extract_specimen_codes($text);
$extra = array();
foreach ($specimens as $code) {
$extra = array_merge($extra, extend_specimens($code, $text));
}
$specimens = array_unique(array_merge($specimens, $extra));
sort($specimens);
if (count($specimens) == 0) {
// none found, insert NULL entry to flag that we've processed this reference
$sql = 'INSERT INTO rdmp_reference_specimen_joiner(reference_id,code) VALUES(' . $reference_id . ',NULL)';
} else {
foreach ($specimens as $code) {
$sql = 'INSERT INTO rdmp_reference_specimen_joiner(reference_id,code) VALUES(' . $reference_id . ',' . $db->qstr($code) . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
}
}
/*
$nm = bhl_names_in_reference_by_page($reference_id);
$nm->names;
// Get majority rule taxon (what paper is about)
$tags = array();
foreach ($nm->names as $name)
{
$tags[] = $name->namestring;
}
$paths = get_paths($tags);
$majority_rule = majority_rule_path($paths);
$expanded = expand_path($majority_rule);
print_r($expanded);
*/
return $specimens;
}
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($reference);
}
}
echo '</ul>';
echo '</li>';
}
echo '</ul>';
}
}
function reference_to_atom($reference, &$feed, &$rss)
{
global $config;
$entry = $feed->createElement('entry');
$entry = $rss->appendChild($entry);
// title
$title = $entry->appendChild($feed->createElement('title'));
$title->appendChild($feed->createTextNode($reference->title));
// link
$link = $entry->appendChild($feed->createElement('link'));
$link->setAttribute('rel', 'alternate');
$link->setAttribute('type', 'text/html');
$link->setAttribute('href', $config['web_root'] . 'reference/' . $reference->reference_id);
// dates
$updated = $entry->appendChild($feed->createElement('updated'));
$updated->appendChild($feed->createTextNode(date(DATE_ATOM, strtotime($reference->updated))));
$created = $entry->appendChild($feed->createElement('published'));
$created->appendChild($feed->createTextNode(date(DATE_ATOM, strtotime($reference->created))));
// id
$id = $entry->appendChild($feed->createElement('id'));
// $id->appendChild($feed->createTextNode('urn:uuid:' . uuid()));
$id->appendChild($feed->createTextNode($config['web_root'] . 'reference/' . $reference->reference_id));
$description = '';
$description .= '<div>';
$description .= reference_authors_to_text_string($reference) . '<br/>';
$description .= reference_to_citation_text_string($reference);
$pages = bhl_retrieve_reference_pages($reference->reference_id);
if (count($pages) > 0) {
$description .= '<div><img src="http://biostor.org/bhl_image.php?PageID=' . $pages[0]->PageID . '&thumbnail" /></div>';
}
$description .= '</div>';
// content
$content = $entry->appendChild($feed->createElement('content'));
$content->setAttribute('type', 'html');
$content->appendChild($feed->createTextNode($description));
// summary
$summary = $entry->appendChild($feed->createElement('summary'));
$summary->setAttribute('type', 'html');
$summary->appendChild($feed->createTextNode($description));
}
<?php
require_once '../db.php';
$id = $_GET['id'];
$query = $_GET['q'];
$callback = '';
if (isset($_GET['callback'])) {
$callback = $_GET['callback'];
}
$obj = new stdclass();
//$obj->matches = 0;
$obj->results = array();
$obj->query = $query;
$bhl_pages = bhl_retrieve_reference_pages($id);
$sql = 'SELECT distinct page FROM rdmp_documentcloud WHERE ocr_text LIKE ' . $db->qstr('%' . $query . '%') . ' ORDER BY page ' . ' LIMIT ' . count($bhl_pages);
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
while (!$result->EOF) {
$obj->results[] = (int) $result->fields['page'];
$result->MoveNext();
}
//$obj->matches = count($obj->results);
header('Content-type: text/plain');
if ($callback != '') {
echo $callback . '(';
}
echo json_encode($obj);
if ($callback != '') {
echo ')';
function bhl_geocode_reference($reference_id)
{
$pages = bhl_retrieve_reference_pages($reference_id);
foreach ($pages as $page) {
$text = bhl_fetch_ocr_text($page->PageID);
$pts = points_from_text($text);
//echo $page->PageID;
//print_r($pts);
if (count($pts) > 0) {
foreach ($pts as $pt) {
$loc = new stdclass();
$loc->name = '';
$loc->latitude = $pt->latitude;
$loc->longitude = $pt->longitude;
$locality_id = db_store_locality($loc);
bhl_store_locality_link($page->PageID, $locality_id);
}
} else {
// No localities
bhl_store_locality_link($page->PageID, 0);
}
}
}
function DisplayText()
{
$text = '';
if (db_reference_from_bhl($this->id)) {
$pages = bhl_retrieve_reference_pages($this->id);
$page_ids = array();
foreach ($pages as $p) {
$page_ids[] = $p->PageID;
}
$text = bhl_fetch_text_for_pages($page_ids);
$text = str_replace('\\n', "\n", $text);
$text = str_replace("\n ", "\n", $text);
// wiki experiments
/*
foreach ($page_ids as $page)
{
$names = names_in_page($page);
print_r($names);
}
*/
}
header("Content-type: text/plain; charset=utf-8\n\n");
echo $text;
}
/**
* @brief Display a set of BHL pages for a reference
*
* @param reference_id Primary key of reference in local database
* @page_to_display Specific page to display (default is 0, which means display first page in reference)
*
* @return HTML for viewer
*/
function bhl_reference_viewer($reference_id, $page_to_display = 0)
{
$pages = bhl_retrieve_reference_pages($reference_id);
//print_r($pages);
echo bhl_viewer($pages, $page_to_display);
}
function DisplayRSS()
{
global $config;
log_access($this->id, 'rss');
// Create XML document
$feed = new DomDocument('1.0', 'UTF-8');
$rss = $feed->createElement('rss');
$rss->setAttribute('version', '2.0');
$rss->setAttribute('xmlns:media', 'http://search.yahoo.com/mrss/');
$rss = $feed->appendChild($rss);
// channel
$channel = $feed->createElement('channel');
$channel = $rss->appendChild($channel);
$title = $channel->appendChild($feed->createElement('title'));
$title->appendChild($feed->createTextNode($this->GetTitle()));
$description = $channel->appendChild($feed->createElement('description'));
$description->appendChild($feed->createTextNode("Page images from " . $this->GetTitle()));
$link = $channel->appendChild($feed->createElement('link'));
$link->appendChild($feed->createTextNode($config['web_server'] . 'reference/' . $this->id));
$pages = bhl_retrieve_reference_pages($this->id);
foreach ($pages as $page) {
$image = bhl_fetch_page_image($page->PageID);
$item = $channel->appendChild($feed->createElement('item'));
$title = $item->appendChild($feed->createElement('title'));
$title->appendChild($feed->createTextNode('Page ' . $page->PageID));
$link = $item->appendChild($feed->createElement('link'));
$link->appendChild($feed->createTextNode($image->url));
$thumbnail = $item->appendChild($feed->createElement('media:thumbnail'));
$thumbnail->setAttribute('url', $image->thumbnail->url);
$content = $item->appendChild($feed->createElement('media:content'));
$content->setAttribute('url', $image->url);
}
// Dump XML
header("Content-type: text/xml; charset=utf-8\n\n");
echo $feed->saveXML();
}
/**
* @brief Create PDF for a reference
*
* We create a simple cover page for the PDF. This page contains basic bibliographic metadata
* for the PDF, in order for Mendeley to process the PDF correctly. In response to my discovery
* that Mendeley doesn't accept all XMP (Ticket#2010040110000015) support@mendeley.com replied that
* they have some heuristic tests to see if the metadata is valid, such as whether the information
* about the title and authors occurs on the first of the PDF.
*
*
* @param reference_id Reference id
* @param pdf_filename Full path of PDF file to create
*
*/
function pdf_create($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, $tags);
}
function bhl_names_in_reference_by_page($reference_id)
{
global $db;
$names = new stdclass();
$pages = bhl_retrieve_reference_pages($reference_id);
// If we don't have a page range then we can't get taxa
if (count($pages) == 0) {
return $names;
}
$names->found = array();
$names->names = array();
$count = 0;
foreach ($pages as $page) {
$sql = 'SELECT * FROM bhl_page_name
WHERE PageID=' . $page->PageID;
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __LINE__ . "]: " . $sql);
}
while (!$result->EOF) {
$namestring = $result->fields['NameConfirmed'];
$namebankID = $result->fields['NameBankID'];
// Have we processed this name before?
if (!isset($names->found[$namestring])) {
$n = new stdclass();
$n->namestring = $namestring;
$n->identifiers = new stdclass();
$n->identifiers->namebankID = (int) $namebankID;
$n->pages = array();
$names->names[] = $n;
$names->found[$namestring] = $count++;
}
$index = $names->found[$namestring];
$names->names[$index]->pages[] = (int) $page->PageID;
$result->MoveNext();
}
}
//ksort($names);
return $names;
}
echo $v[$i] . ' (' . $v[$i + 1] . ')';
echo '</li>';
}
echo '</ul>';
echo '</li>';
}
echo '</ul>';
echo '</td>';
// Hits
echo '<td valign="top">';
echo '<table>';
foreach ($hits->response->docs as $doc) {
echo '<tr>';
echo '<td>';
if (preg_match('/reference\\/(?<id>\\d+)/', $doc->id, $m)) {
$pages = bhl_retrieve_reference_pages($m['id']);
if (isset($pages[0]->PageID)) {
$image = bhl_fetch_page_image($pages[0]->PageID);
$imageURL = $image->thumbnail->url;
echo '<img style="border:1px solid rgb(192,192,192);" src="' . $imageURL . '" width="40" />';
} else {
echo '<img style="border:1px solid rgb(192,192,192);" src="' . $config['web_root'] . 'images/blank70x100.png' . '" width="40" />';
}
}
echo '</td>';
echo '<td valign="top">';
echo '<span><a href="' . $doc->id . '">' . $doc->title . '</a></span><br />';
echo '<span style="color:green;font-size:12px;">';
$str = $hits->highlighting->{$doc->id}->citation[0];
$str = str_replace('<em>', '<b>', $str);
$str = str_replace('</em>', '</b>', $str);
